DomainBuilder User Manual Table of Contents
Contents
1. DomainBuilder User Manual Table of Contents te GCI ot OD rse 3 LONO ID ssa EE Ea Ea aE 3 Becoming an Authenticated User WE 3 Opening Doman BUTS sissi iiisnnnaianaaan aaua aaa aaora a Aaa i Ra a AAR TGNA aa 4 Greate a New Knowledge BAS 6 isastest annaa aanraai A Ea AERAR EARE ana 4 Browse an Existing Knowledge Base csscsessssssssesesesesseseseeseseseseeseneseseseeneneeseseenensaeaeaseneneaeaeeneneneaeaeens 4 Importing an Existing Knowledge Base csessssscsesssssseseseesessseseesesesseseesenesesessenenseaeaseneneeaeeseneneaeasens 4 Exporting an Existing Knowledge Base ccssssssesecsessssseseesessseseseenessseasenessiesesseneneeaesseneneeaseneneneaeaeens 4 Deleting an Existing Knowledge BaSe cscsssssssesecsssssseseesssseseesessseesseseseieacssenenseacasenensaeaseseneaeaeacens 4 Using Nenu Trees to Select Etgen EENEG 5 Locating Items in th Menu Ke 5 Selecting an Item trom th Menu TEE asninn eaea AaS aeania 5 Case TaD E 6 Case Maint EE Te 6 Creatine ad NOW E 6 lee et 7 dM GAG ert cuss srdataceneasiteuasa nah A S isu oetartrinbiayess 7 TA OTT EE 8 E poria E 8 Adding Clinical Report Jotormafom zeegt EERSTEN 8 riet ne AREPO SE 8 Cut Copy Paste in the Report d 9 SPO SMES O aa E A E E EO 10 Using a Worksheet to Input Clinical Information ee 10 Parne MER TO EE 10 Adding Concepts to the Knowledge Base from the RepoTft s s ssrsssressrsnrrssrensnensnnnrnnsnensnennnes 10 Adding Removing Knowledge Base Concepts2. Select Case Domain Ato slidetutor Up eduicurriculumowlskinJP PervascularDermatitis owl Diagnoses Cases Report ALL DIAGNOSIS AP_607 PATIENT HISTORY ALLERGIC CONTACT DERMATITIS AP 611 The patient if a 66 year old male Medial aspect of lett ARTHROPOD ASSAULT AP 615 thigh looks like inverse pityriasis rosacea BULLOUS_ PEMPHIGOID AP_629 FINAL DIAGNOSIS CANDIDIASIS AP_695 SKIN MEDIAL ASPECT OF LEFT THIGH SHAVE CHONDRODERMATITIS_NODULARIS_H AP_f09 BIOPSY DERMATITIS_HERPETIFORMIS AP_f13 DERMATOPHYTOSIS see comment DERMATITIS_HERPETIFORMIS LIKE_D PD_13 SEN DERMATOMYOSITIS PD_18 Presence a hyphae and spores is seen even on HE DERMATOPHYTOSIS PL_11 stained sections DISCOID_LUPUS ERYTHEMATOSUS PL_14 DISSEMINATED _SUPERFICIAL_ACTINIC PL_15 GROSS DESCRIPTION DRUG_ERUPTION PL_16 taggen DYSHIDROTIC_DERMATITIS PL_17 4 D PL_19 S AP_713_HE Search by Case Name AP_ f13 Slides The cases are colored based on the Case Status see Case Status section below Incomplete cases are displayed in red Complete cases are displayed in blue Tested cases are displayed in green Saving a Case If you are an authenticated user saving a case will save the file in your local cache as well as upload it to the curriculum server If you are not an authenticated user the file will only be saved to the local cache To save a case 1 Click the button C for authenticated users OR select Save from the File
3. WARNING required action not specified L4 MALIGNANT MELANOCYTIC LESION properties remove up down 4 domain http slidetutor upme edufcurriculumiowl skin PITT Melanocytic owl user not authenticated from PITT Creating a New Template To create a new report template 1 Click the button in the Templates area of the screen OR right click in the Templates list area and select the Add Template option 2 Type in a name for the template 3 Click OK Deleting a Template Report templates can be deleted from the Knowledge Base To delete a template 1 Click the template to select it 2 Click the button in the Templates area of the screen OR right click and select the Remove Template option Reportable Items Reportable Items are a list of concepts that you would like the ITS to monitor the student s ability to assess and include in a prognostic report 34 Adding Reportable Items To add a Reportable Item click on the hada Reportable Items button either in the middle of the template or on the menu bar at top Select the appropriate concept s in the order you would like the items to appear in the student s report Click OK Deleting Reportable Items To remove a Reportable Item click on the remove link to the right of the concept you would like to be deleted Reorder Reportable Items After Reportable Items are added to a template they can be reordered To increase the pr
4. E Gi S Ka domain http slidetutor upme edu curriculumowl skin PIT T PerivascularDermatitis owl user not authenticated from PITT Adding Diagnoses The Diagnosis Builder tab is empty when it is first opened The first step is to add the diagnoses you want to build To add diagnoses 1 Click the oF button 2 Select the desired item s from the menu tree that appears AUTHORING NOTE If you would like to see all of your diagnoses that were previously worked on you must individually add each and every diagnosis that you would like to see Adding Findings to Diagnoses Once diagnoses have been added you can add findings to diagnoses saying what findings a particular diagnosis must have or must not have To add findings 1 Start typing already existing findings and selecting the appropriate finding from the combo box OR 30 1 Right click and choose Add Finding 2 Select the appropriate finding s from the tree 3 Click OK Modifying Rules for Findings When findings are initially added to a diagnosis they indicate that this one finding is present for that diagnosis The default is for cells to be ANDed meaning all of the findings listed must be present However findings can be modified to mean other things you can indicate that a finding is not present for a diagnosis and you can indicate that you have to have either one finding OR another finding i
5. menu 2 If the Enter Case Name popup appears type in an appropriate name for the case and click OK Importing a Case Cases can be imported from previously saved case files stored locally on your computer To import a case file 1 Click the button OR select Import from the File menu 2 Select the file you wish to import 3 Click Open Exporting a Case Cases can be exported and saved locally on your computer To export and upload a case 1 Click the button OR select Export from the File menu 2 If the Enter Case Name popup appears type in an appropriate name for the case and click OK 3 Navigate to the folder where you want the case file to be saved 4 Type in a file name for the case file to be saved as in the File Name box if you want it saved as a different name 5 Click Save Adding Clinical Report Information The top right portion of the Case Tab is where clinical report information is added Reports can be added by either typing into the report area or importing a previously saved text file Importing a Report You can import an existing clinical report in a text format txt Some clinical reports may not follow the same conventions used by DomainBuilder That is why the Align Report to a Template dialogue pops up to help users import all relevant clinical information into the format that is understood by the system To import a report 1 Click the RB button OR select Add Report from the C
6. Alt W on your keyboard Annotating Digital Slides Various shapes are available for annotating slides To draw an annotation on a slide 1 Select the appropriate drawing button by either clicking the button or using the appropriate keyboard shortcut 2 Hold down the left mouse button over the slide and move the mouse to draw the shape 3 Release the mouse button Below is a table listing each type of shape available a picture of the button used for drawing it and the keyboard shortcut for selecting the button Shape Button Shortcut 16 Arrow Wi Alt A Rectangle Alt R Oval circle C Alt O Polygon A Alt P Measuring tool gio Alt M Annotations can also be added by choosing the appropriate option from the Annotations menu Once a shape is drawn it will be listed on the Shapes Tab on the right hand side of the screen To delete a shape right click the shape in the list of shapes and select the Delete option Modifying Shapes Shapes that are drawn can be modified using the black boxes that appear on the edges and midpoint of each shape Boxes on the edges can be used to resize or rotate shapes and the midpoint can be used to move the shape to a different area of the slide Simply hold down the left mouse over the appropriate box and drag the mouse to resize rotate or move the shape as desired Cut Copy Paste Shapes You have the ability to cut copy and paste shapes Cutting and pasting shapes under a new tag wi
7. E ER Ke OES i a 35 PGI a TV OCI asiscapacae scl test cen ecicatescachbaeeccits ctscutindecscenteticshbescus ea aaoedebbonnncdanteueaeeneenaics ae atibeneseiatsi ate 35 Deleting a TIS EE 36 EE ees 37 PC RCW Ee 37 Right Chek Ment Options siisssctscsisverscasecansistivansttiscetssehdssvecuinscaacelsuensehisnstecsbavetecsaantvacdieuencdbuasticaetan 37 lee 38 Eeer 38 Open EHEKETHEN ee 38 GREEN 38 Introduction DomainBuilder is a tool designed to create a Knowledge Base and annotate cases that are used by an intelligent tutoring system to provide instruction within a particular pathology domain This process consists of creating editing a Knowledge Base inputting all of the case information and annotating drawing shapes on the digital images Logging In When you first start DomainBuilder you have an option to log in If you log in with valid credentials for a selected institution you will be able to save all of your authoring to the central curriculum server which will make your authoring available to others DomainBuilder Name 7 Password Institution PITT Status Entername and password If the system cannot authenticate you then you will become a not authenticated user which means that all of your authoring will be done in your local cache and will not be visible to others In that case you will receive the warning message below Warning Could not register with the server hittp slidetutor upmec edu domainbuilder und
8. JUNCTIONAL PIGMENTED SPINDLE CELL NEVUS 1 cases of JUNCTIONAL SPITZ NEVUS 1 cases of MALIGNANT MELANOMA IN SITU NOS Case Summary CASE STATUS DIAGNOSES AP_ 1018 Ap 1027 39
9. Knowledge Base highlight the appropriate Knowledge Base and click on D Using Menu Trees to Select Items Throughout DomainBuilder menu trees are used at various times for selecting findings and diagnoses Below is a screenshot of a sample menu tree Findings E en et le o eegen bundles collections of eosinophils cornoid lamellation collections of eosinophils Hi edema i ils eosinophilic inflammatory ir isolated eosinophils f omogenous material 5 1 oh a y a e EE 5 dE dr ES ta D histiocytic giant cells S ypergranulosis interface reaction histiocytic inflammatory infil langerhans cells langerhans cells inflammate yeogranulosis CYTOLOGIC FEATURES OTHER FEATURES ARCHITECTURAL FEATURES Lal Jichencid reaction ffocal lichenold reaction i inflammatory response abnormal lymphocytes lymphocytes isolated lymphocytes lymphocytic inflammatory in 3 D D a ocyt Ail S it HIE SIE L a K o i i mast cells mast cell inflammatory infilt collections of neutrophils E rete ridges i isolated neutrophils scale crustl Lues dust neutrophilic inflammatory in sclerosis plasma cells plasma cell inflammatory in siderophages g a tn 1 an double click adds selected concept to a list Screenshot of Menu Tree for Findings with an Item Selected Locating Items in the Menu Tree There are two ways you can locate
10. complete prognostic report Hierarchy Builder Tab The first sub tab is the Hierarchy Builder tab where you create a hierarchy containing all concepts that go into the knowledge base In this tab you can add concepts to the knowledge base edit arrange concepts in the knowledge base and add edit definitions synonyms and example pictures of concepts When creating a new knowledge base certain concepts will already exist The various concept types ACTIONS ANCILLARY STUDIES DIAGNOSES FINDINGS LOCATION MODIFIERS and VALUES will all be present Additionally specific concepts will be listed under ACTIONS and VALUES i d A ATTRIBUTE d RCTIONS ACLINICAL FINDINGS lt JANCILLARY STUDIES patient gender DIAGNOSES DIAGNOSTIC FINDINGS a CYTOLOGIC FEATURES 3 N FINDINGS OTHER FEATURES E anatomic location j A procedure PROGNOSTIC FINDINGS gess ae excision V tissue WORKSHEET Pre existing concepts in Knowledge Base Adding Concepts To add concepts to the hierarchy 1 Click the appropriate parent concept concept type in the hierarchy to select it NOTE concepts will always be added beneath the selected concept 2 Choose the Add Concept option by either right clicking the selected concept OR 24 choosing Add Concept from the Builder menu 3 In the popup window you can add the concept s you would like to create If you would like to create a hierarchy of concep
11. infiltrate nerve banal melanocytes infiltrate reticular dermis AP 1042 AP1043 AF1044 banal melanocytes infiltrate smooth muscle basilar melanocytes decreased in number basilar melanocytes increased in number AP 1050 AP 1051 basilar melanocytes normal in number SldslsiidsfbsidetelduzEiveleiCH celular cohesion Weni MEE aE SNE AP 1052 AP1055 AP1065 AP124 AP126 AP138 AP 202 AP258 AP 262 AP 267 AP 277 AP 292 BER AP 299 AP 301 AP 302 few mitoses of melanocytes in dermis ielielelistirem fibrosis get Wiga tele eee E genital skin S AP 305 AP 306 AP 307 consumption of epidermis Melali Lere EA Eaire aE EEEE OS EE dendritic melanocytes dendritic melanocytes in reticular dermis dermal scar disordered lentiginous proliferation of melanocytes effaced rete ridges elongated rete ridges enlarged nests of melanocytes in epidermis epithelioid melanocytes increased pigmentation in epidermis inflammatory response inflammatory response with well defined inferior margin AFP 312 AP317 AP 319 junctional clefts kamino body BiiiksllslfCdrsUlOlcCiftslbsgdu EE OSEE AP 321 AP322 AP 323 lentiginous proliferation of melanocytes above scar marked inflammatory response marked pagetoid spread oc ae anaes a AP 333 AP 334 AP 335 marked solar elastosis maturation melanopbades minimal pagetoid spread minimal solar elastosis 1937 AP 338 AP 34 mitoses of melanocytes mitoses of melanocytes in dermis moderate cytologic atypia moderate inflammatory resp
12. select the appropriate tab at the top of the popup window for the information you want to add 3 Click the appropriate radio buttons to select values 4 Repeat steps 2 and 3 as needed 5 Click OK Your selections will be appended to the end of your report in the Final Diagnosis Section Parsing the Report Once a report is entered either typed in or imported it can be processed by clicking the i button At that point any report text that is matched with concepts in the Knowledge Base will turn blue and any Knowledge Base concepts found in the report will be listed appropriately under Diagnosis Findings Report Clinical and or Ancillary Adding Concepts to the Knowledge Base from the Report If there are any concepts that did not parse in the report you can add the concept from the report text directly to the knowledge base To add report text to the Knowledge Base 1 Highlight the text in the report 2 Right click the highlighted text 3 Choose Suggest Term from the drop down menu 10 Select Diagnositc Findings Search withthe ANCILLARY STUDIES arrere D CONCEPTS m N ENG i ARCHITECTURAL FEATURE Ena FINDINGS FINDINGS DIAGNOSTIC FINDINGS Les CYTOLOGIC FEATURES RECOMMENDATIONS PROGNOSTIC FINDINGS aa THER FEATURES double click adds selected conceptto a list A ARCHITECTURAL FEATURES If the highlighted text is a synonym for an existing concept 1 Highlight the text in
13. that are true for that individual case For example if the set of findings X or Y is associated with the diagnosis of Bullous Pemphigoid and only Y is present in the case then you would want to assert concept Y to inform the ITS that Y is indeed part of the case Asserted concepts have a green border around them Concepts that are parsed through the report or manually added to the case will automatically be asserted To manually assert a concept you can right click the concept and choose Assert Concept from the menu Recommendations Advice In some tutoring systems it may be desirable to associate recommendations or advice with a diagnosis or a finding in the tutoring case For example if recommendation concept use steroid cream is associated with diagnosis acute burn then the tutoring system may do additional tutoring incorporating that recommendation if that diagnosis is observed Validating Knowledge Base Concepts for a Case After completing the case authoring click on the iM button to check that the case information is consistent with the Knowledge Base content for a disease If the information authored is NOT consistent with what is in the Knowledge Base DomainBuilder will add any missing concepts to your case OR it will give youa warning message telling you what is inconsistent Adding Additional Pathologies to the Case Some cases may have multiple unrelated diagnoses on one or several slides within the same case These
14. 9 Transform d Brightness Contrast Crop Original Image sS A Flip Flip Vertically Horizontally To change the brightness or contrast of a slide 1 Click the button 2 Make sure that the Brightness Contrast tab is selected and move the sliders to set the desired brightness and or contrast Transformation Properties Transformations and Filters E Transform d Brightness Contrast V SE eege To crop a slide 1 Click the button 15 Target Image d si G Ta SC Kl eer ae h hee ie Co x SSE e NE d AS vg etzd oe oy GA KR r ees 4 lt lt e On y Zu e d WS 8 Original Image 2 Make sure that the Crop tab is selected 3 Click the Crop Image button and set box to desired points to crop the image Transformation Properties Transformations and Filters Target Image Transform f Brightness Contrast H crop ii W Crop image Original Image SI Revert Image Cancel If at any time you want to go back to the original image click the Revert image button at the bottom of the window When this button is selected it will undo of all the transformation that were made to the slide Expand Digital Slide Area The viewer area can be expanded by clicking the H button or pressing Alt W on your keyboard The viewer area will open in a popup window To close the expanded viewer area Click the H button again or press
15. NG NOTE Multiple slides can be loaded at the same time by using shift click to select slides listed consecutively or control click to select slides not listed consecutively You can author digital slides from different locations institutions by using the location drop down menu in the open slide dialog box 3 Click OK All loaded slides will appear in the slide list on the right hand side of the screen Click on a thumbnail to change slides Navigating Digital Slides DomainBuilder incorporates a virtual microscope that has similar functions as a regular microscope but operates using a mouse Move around Slide To move around the slide press and hold the left mouse button Drag the mouse then release the mouse button Repeat until the desired area is in view Zoom In Out To zoom in Left click the RW button OR click the mouse over the image To zoom out 13 SS Left click the button OR right click the mouse over the image You can also zoom in and out using the scroll wheel on your mouse when your mouse is over the image To return to the whole slide view click the ston Refresh Digital Slide If the viewer is not refreshing allow a few seconds for the new view to appear If o that does not help click the button and try using the viewer again sometimes resetting the viewer helps Magnifier Window The Magnifier window provides a small window that shows a portion of the slide at a higher magnific
16. a Trigger To delete a trigger 1 Select the trigger that is to be deleted 2 Click the button Validation Tab The Validation Tab allows you to verify information in the knowledge base and individual cases By mousing over a particular item all items of other types containing that item will by highlighted For example if you mouse over a finding all diagnoses and cases containing that finding will be highlighted If you mouse over a particular diagnosis all findings that disease contains according to the knowledge base and all cases with that diagnosis will be highlighted If you mouse over a particular case all findings and diagnoses that case contains according to the authoring will be highlighted In this way information in the knowledge base and individual case authoring can be checked and validated before being used in the tutoring system 36 DomainBuilder File Options Help Knowledge Validation Te Search og Findings acanthosis of epidermis acral skin asymmetrical Eil atrophy of epidermis atypical melanocytes AP 1018 AP1027 AP 1029 ms AP 1031 AP 1032 solkors MEIO CERE CR GUIEN atypical melanocytes infiltrate eccrine ducts atypical melanocytes infiltrate follicles AP 1033 AP 1034 AP 1037 atypical melanocytes infiltrate papillary dermis atypical melanocytes infiltrate subcutis balloon cells banal melanocytes AP 1040 AP 1041 banal melanocytes infiltrate dermis banal melanocytes
17. ase menu OR right click a particular shape and choose the Add Tag option NOTE using the right click method will automatically move that shape under the tag being created 2 Type in the name of the tag 3 Click OK To create multiple tags at once 1 Click the button in the shapes tab 2 Type in each name of a tag separated by a comma 3 Click OK Delete a Tag To delete a tag 1 Select the tag you would like to delete 2 Click on the button or Right click on the tag and select Delete Any shapes associated with that tag WILL NOT be deleted They will be moved underneath the default tag Untagged Organizing Annotations with Tags To associate untagged annotations to a single tag 1 Select the shapes you would like to associate with a tag 2 Drag and drop hold down the left mouse button and drag shapes to the appropriate tag Ifa shape s are already associated with a tag they can also be copied to another tag To associate shapes to an additional tag 1 Select the shapes you would like to associate with an additional tag 2 Click the button 3 From the pop up window select the additional tag you would like the shape s to be associated 4 Click OK 18 Case Authoring for SlideTutor ITS The case authoring process for SlideTutor ITS is unique from the standard authoring of digital slides In order to ensure the case content will work properly in the ITS it is imperative that you first understan
18. ase menu 2 Locate the file you want to import 3 Click Open 4 Use the Align Report to Template dialogue to select the sections that you want to add to the Target Report in case they were not extracted automatically Allen Report to a Template Align Report to a Template Align sections from the imported Source report to the target report template by eher 1 Copying pasting text from source report into relevant sections of the target report 2 Highlighting relevant text in the source report right clicking on the highlighted text and selecting an apporpriate section of the target report Source Report HISTORY 45 year old female with bleeding pigmented lesion on arm REPORT SECTIONS DIAGNOSIS SKIM ARM EXCISION MALIGNANT MELANOMA IM THE EPIDERMIS O FINAL DIAGNOSIS PAPILLARY AND RETICULAR DERMIS NMVAGI COMMENT ULCERATION IS IDENTIFIED RADIAL GROWTH PHASE PRESENT VERTICg GROSS DESCRIPTION FRESENT MICROSCOPIC CLARKS LEVEL IY BRESLOW DEPTH 1 36 Ml MITOTIC INDEX 6 PER 10 HFF TUMOR INFILTRATING LYMPHOCYTES BRISK VASCULAR INVASION PRESENT DERMAL MEVUS PRESENT INVOLVING DEEP MARGIN LATERAL PATIENT HISTORY Target Report PATIENT HISTORY FINAL DIAGNOSIS lected text into PATIENT HISTORY Insert s GROSS DESCRIPTION Received in formalin and labeled lesion the specimen consists of one small ellipse measuring 0 80 3 2 0 3 cm There is a central pigmented lesion with raised center The specime
19. ation To open the Magnifier window click the button The mouse cursor changes to a box Move your mouse cursor over the slide to view different areas of the slide in the Magnifier window or drag the magnifier window itself over the area of the slide that you want to magnify To close the Magnifier e window click the button again Navigator window The Navigator window provides a smaller view of the entire slide that you can use to see where you are on the slide and to control what is displayed in the main window To open the Navigator window click the 5 button The area of the slide you are viewing has a box around it You can move to a different area of the slide using the Navigator window by clicking on a different area or by dragging the box around by pressing and holding the mouse button and dragging the mouse To close the Navigator window click the k button again Modifying Digital Slides The digital slides can be modified in the context of the case They can be rotated flipped or and cropped Users can also adjust the brightness and contrast All of the changes are not persisted on the original digital slide but are stored within the case and only work within the context of the case To transform the orientation of a slide Ld 1 Click the 4 button 2 Make sure that the Transform tab is selected and select the rotation that you desire 14 Transformation Properties Transformations and Filters Target Image
20. create a worksheet 1 Click on PROGNOSTIC FINDINGS in the Knowledge tree 2 Right Click on WORKSHEET 3 Click Add Concept 4 Type in the concept hierarchy for the worksheet that you would like to create Below is a screen shot of an example hierarchy of pathologic staging of melanoma 28 Create New Concepts Enter a List of Concepts 1 Pathologic Staging pT HT 1 pTia pTib ple Hho DN Sei HINT enter each concept on a new line use tabs to indicate hierarchy a E O Ss oS on ds LA mm k Once all the information is entered along with definitions the end result will look something like this Worksheet pathologic staging gt pTO No evidence of primary tumor pTi Melanoma 1 0 mm or less in thickness with or without ulceration 2 pT1a Melanoma 1 0 mm orless in thickness no ulceration 1 mitoses mm2 gt pT1b Melanoma 1 0 mm or less in thickness with ulceration and or 1 or more mitos pl2 Melanoma 1 01 to 2 0 mm in thickness with or without ulceration O pT2a Melanoma 1 01 to 2 0 mm in thickness no ulceration gt pT2b Melanoma 1 01 to 2 0 mm in thickness with ulceration pls Melanoma 2 01 to 4 0 mm in thickness with or without ulceration 2 pT3a Melanoma 2 01 to 4 0 mm in thickness no ulceration gt pT3b Melanoma 2 01 to 4 0 mm in thickness with ulceration pl4 Melanoma greater than 4 0 mm in thickness with or without ulceration gt pT4a Melanoma greater than 4 0 mm in t
21. d selecting or deselecting the appropriate pathologies Viewing Different Pathologies In order to view different findings and diagnoses that are associated with different pathologies 1 Click on the L amp button or select Other Pathology from the case menu 2 Select a pathology description that you would like to view Once a pathology is selected all findings and diagnoses that are not associated with the selected pathology will be grayed out To return to original display select the All Pathologies option from the same menu Case Status The case status is set for case management purposes so that the author will know which cases are ready to be deployed which cases still need to be tested and which cases Still have authoring issues associated with them 23 To mark the status of a case 1 Select Case Status in the Case menu or Click the 41 button 2 Select the appropriate status from the list Incomplete Complete Tested Knowledge Tab The Knowledge Tab is where all of the creating and editing of knowledge base information is handled and contains three sub tabs e Hierarchy Builder This tab allows concept creation and the organization of concepts into a tree like structure e Diagnosis Builder This tab allows you to link diseases with its associated findings and visualized the similarities and differences between them e Report Builder This tab allows you to create report templates to help guide a student in writing a
22. d the ITS requirements Locations Annotations The first annotation requirement is the list of Locations annotations These annotations must have an area s of the digital slide associated with them Typically freehand polygons rectangles and circles are used as Locations The Locations annotations are used to monitor where a student can identify a particular Knowledge Base concept and also provide assistance to the student on where he she should look for a particular concept To learn how to add shape s tag s as a Location Annotation see the Linking Annotations with Knowledge Base Concepts section below Case Concept Properties interface reaction Assert Concept in Case _ Mark as Explicitly Absent Concept in Case Feature Prime Example in Case a use All Locations where Case Concept can be observed A Arrow29 d Polygon9 Polygon Polygons Polygons Polygon 4 Polygon 1 Polygoni9 Polygont7 Polygont5 Polygon13 Polygonti Polygont All Recommendations Advice associated with this concept 19 This is the area of lymphocytes more Prime Example Annotations The second annotation requirement is the Prime Example annotation The prime example annotation can be any type of shape However arrows are the most common form of Prime Example annotation The Prime Example annotations are used to point to an exact location of a concept To learn how to add shape s tag s as a Prime Example an
23. d to a diagnosis by importing a Comma Separated Value csv file into DomainBuilder Comma Separated Value files can be created through applications such as Microsoft Excel To create a csv file 1 Create a spreadsheet with the first row of each column being the diagnosis and each subsequent row the appropriate findings associated with the diagnosis COMPOUND MELANOCYTIC INTRADERMAL JUNCTIONAL NEVUS MELANOCYTIC NEVUS MELANOCYTIC NEVUS lentiginous proliferation of lentiginous proliferation of melanocytes OR junctional nest melanocytes in dermis OR nest of melanocytes OR junctional nest of melanocytes melanocytes in dermis of melanocytes Ft ll reall E melanocytes in dermis melanocytes NO melanocytes in dermis No sgicagpia Jet dmg NO cytologic atypia melanocytes dermis NO pagetoid spread NO cytologic atypia So maturation maturation AUTHORING NOTE In order to create an OR ed rule simply place OR in caps between the two features In order to create an absent finding simply place NO in all caps before the concept 2 In the menu click on File and then Save As Enter in the name of the file and make sure to choose CSV or Comma Separated Value as the file type 3 Open DomainBuilder and create open the appropriate Knowledge Base 4 Click on the Knowledge Tab and then the Diagnosis Builder Tab 5 Click on and browse for the csv file Click OK NOTE Please be patient It can take several minutes to create and imp
24. e item and selecting the Unbookmark option Open Option The Open option allows you to jump to a particular concept in the knowledge base or open a case from the Validation Tab To go directly to a concept or case from the Validation Tab simply right click the appropriate item and select the Open option Summary A case summary is available that provides basic statistics of cases that are in DomainBuilder To access this case summary click on the button in the upper left hand corner of the Validation Tab 38 Domain Summary 171 total cases O cases authored 31 cases tested 2 Cases pending completion Diagnosis Summary 3 cases of COMMON BLUE NEVUS 2 cases of COMPOUND ATYPICAL MELANOCYTIC NEVUS 2 cases of COMPOUND CONGENITAL MELANOCYTIC NEVUS 2 cases of COMPOUND MELANOCYTIC NEWUS 3 cases of COMPOUND PIGMENTED SPINDLE CELL NEVUS 1 cases of COMPOUND SPITZ NEVUS 1 cases of IN SITU AND INVASIVE ACRAL LENTIGINOQUS MALIGNANT MELANOMA 1 cases of IN SITU AND INVASIVE LENTIGO MALIGNA MELANOMA 4 cases of IN SITU AND INVASIVE MALIGNANT MELANOMA NGS 2 cases of IN SITU AND INVASIVE NODULAR MALIGNANT MELANOMA 3 cases of IN SITU AND INVASIVE SUPERFICIAL SPREADING MALIGNANT MELANOMA 2 cases of IN SITU LENTIGO MALIGNA MELANOMA 1 cases of INTRADERMAL CONGENITAL MELANOCYTIC NEVUS 1 cases of INTRADERMAL MELANOCYTIC NEVUS 1 cases of JUNCTIONAL ATYPICAL MELANOCYTIC NEWUS 2 cases of JUNCTIONAL LENTIGINOUS MELANOCYTIC NEVUS 1 cases of
25. e the appropriate shape or tag from the popup that appears Concepts that have only Location annotations OR Prime Example annotation linked with it it will turn yellow Once a concept has both a Prime Example annotation and Locations annotations linked to it it will turn green Case Concept Properties Properties of concepts within a particular case include the annotations linked with that concept whether that concept is asserted has all appropriate annotations linked with it and whether the concept is present or explicitly absent in the case 21 Viewing Case Concept Properties To view properties for a particular concept double click that concept A popup window will appear showing the properties for that concept To view the properties of all concepts of a particular type diagnoses findings or prognosis click the button Each concept will be listed as a tab at the top of the popup window Modifying Linked Annotations Using Case Concept Properties Additional annotations can be linked to a concept using the Case Concept Properties popup window by dragging shapes or tags from the Shapes list to the appropriate box in the popup or by using the appropriate F button and selecting the shape or tag from the popup window that appears Annotations can also be unlinked by clicking the annotation in the Case Concept Properties popup window and clicking the appropriate button Asserted Concepts Asserted concepts are concepts
26. er username You will NOT be able to upload example images exported cases or ontologies Becoming an Authenticated User Contact the DomainBuilder administrator to gain log in credentials Opening DomainBuilder Once DomainBuilder loads a popup will appear with several options Open Domain Institiution E Organ Domain bladder Alopecia owl breast Carcinoma owl dinosaur EpidermalCysts Tumors owl prostate FibrosingDermatitis owl Melanocytic ow NodularDiffuseDermatitis owl Panniculitis owl PeriinftundibultisPerifolliculttis owl PertvascularDermatitis owl BPusctilarnearmatitic oul OK Cancel Create a New Knowledge Base To create a new knowledge base click on LA Fill in the appropriate fields and click OK Browse an Existing Knowledge Base To browse the contents of an already existing Knowledge Base select the appropriate Knowledge Base and then click on amp A popup will appear with all of the existing concepts within the Knowledge Base To navigate through the concepts simply click on a parent concept to open the children concepts in a new column to the right of the parent concept Importing an Existing Knowledge Base To import an existing Knowledge Base in the owl format click on a Exporting an Existing Knowledge Base To export an existing Knowledge Base in the owl format highlight the appropriate Knowledge Base and click on Op Deleting an Existing Knowledge Base To delete an existing
27. hickness no ulceration 2 pT4b Melanoma greater than 4 0 mim in thickness with ulceration gt pTx Primary tumor cannot be assessed teg shave biopsy or regressed melanoma gt pTis Melanoma in situ de not an invasive tumor anatomic level D DN egional Lymph Nodes O pid No regional ymph node metastasis pN1 Metastasis in 1 regional lyinph node Diagnosis Builder Tab The next sub tab is the Diagnosis Builder tab which allows you to say what findings each disease has and to compare findings in different diseases and see similarities and differences between them Diseases can have multiple distinct feature sets 29 DomainBuilder File Edit Builder Tools Help D Case amp Knowledge Validation EB dh el ems HEEL vor we NO interface reaction NO interface reaction interface reaction NO ballooning NO ballooning vacuolar reaction moderate lymphocytic inflam NO spongiosis NO spongiosis _ Oe marked lymphocytic inflammat NO psoriasiform acanthosis NO psoriasiform acanthosis epidermal necrosis of isolated NO eosinophilic inflammatory NO lymphocytic inflammatory i minimal eosinophilic inflamm minimal perivascular lymphoc ballooning moderate eosinophilic inflam moderate perivascular lympho isolated neutrophils in dermis _ Of lt lt parakeratosis isolated eosinophils in dermis Q E D EH D E r Q a a wn gt s i 2 F ke
28. ing diz Replace with Finding Report Builder Tab The last sub tab in the Knowledge Tab is the Report Builder tab which contains templates for writing prognostic reports In this tab you can create and edit templates and assign individual prognostic findings to a template 33 DomainBuilder File Edit Builder Tools Options Help amp Knowledge E Validation i S d d E Add Reportable Items Templates Triggers in the Template l I I E L OR invasive lesion template g KR IN SITU AND INVASIVE ACRA H DESMOPLASTIC MALIGNANT or IN SITU AND INVASIVE MALIG or INVASIVE MALI atypical lesion template EA 4 Ill gt in situ lesion template Reportable Items in the Template benign lesion template a tissue properties remove up down n anatomical structure consisting of similarly specialized cells and intercellular matrix aggregated according to genetically determined spatial relations performing a specific function skin WARNING required action not specified Report Builder Diagnosis Builder Hierarchy Builder 2 anatomic location properties remove up down Named locations of or within the body Possible Values buccal labial location a oral WARNING required action not specified 3 procedure properties remove up down Any medical procedures that are relevant to the medical domain Possible Values punch shave wide
29. instances should be marked so that the system can distinguish between the unrelated diagnoses 22 Creating and Deleting Additional Pathologies Before you can add additional pathologies to unrelated diagnoses you must first create it To create additional pathologies 2 Click on the L button or select Other Pathology from the case menu 3 Click on Add Other Pathology 4 Typea description of the pathology being added in the popup window 5 Click OK Once you have added your additional pathologies they will be available for selection the Other Pathology menu You can remove unwanted pathologies by clicking Remove Pathology and selecting the pathology that you want to remove from the drop down menu and clicking OK Marking Unrelated Diagnoses with Respective Pathologies Once new pathologies have been added you can mark the unrelated diagnoses with their respective pathologies to tell the system that the case diagnoses are in fact unrelated to each other and do not constitute a differential diagnoses To mark unrelated diagnoses with their respective pathologies 1 Right click on a diagnosis 2 Select Pathologies sub menu 3 Click to check off pathologies that apply to the diagnosis AUTHORING NOTE When a pathology is added to a diagnosis all findings that are associated with that diagnosis will automatically be marked with the same pathology You can manually set pathologies for individual findings by right clicking them an
30. iority of a Reportable Item click the up link at the right of the concept to move the concept up one position Continue clicking the up link until the concept is in the desired position To decrease the priority of a Reportable Item click the down link at the right of the concept to move the concept down one position Continue clicking the down link until the concept is in the desired position You can also reorder reportable items by changing the order number to the left of the item Triggers Each template needs to be assigned triggers to indicate when the template should be used Adding a Trigger To add a trigger 2 Click on the button under Triggers in the Template heading 3 Select the appropriate conditions that will activate this report template 4 Select OK The default is for triggers to be ANDed meaning all triggers must be present for the template to be triggered You can also use the OR or NO to create more complex triggers scenarios within the template 35 AUTHORING NOTE Triggers are the conditions upon which a template is activated For instance if there is one format for reporting about a needle core biopsy of adenocarcinoma and another format for reporting about a resection of adenocarcinoma you would create one template that has the triggers Adenocarcinoma and Needle core biopsy and another template with the triggers Adenocarcinoma and Resection Deleting
31. items in the menu trees opening and closing the tree or typing in a string to search for in the tree To expand the tree click a branch of the tree and that branch will open to display its contents Branches that can be opened are indicated by a triangle or rectangle on the right of the item To open another branch click on the expandable item Alternatively you can have the program search the tree for a particular string of letters by typing the string in the search box and clicking Go or pressing the enter key on your keyboard The tree will highlight in orange any items containing that string To go back to the original view of the tree click the Reset button Selecting an Item from the Menu Tree To select items from the menu tree 1 Do one of the following 1 Click on the item to highlight it and click the F button 2 Right click the item 3 Double click the item 2 Repeat step 1 to add additional items to the selection list as desired 3 Click OK Even if the item appears to be highlighted from using the search tool you still need to click the item to make sure it is selected To remove an item from the selection list 1 Click on the item to highlight it Make sure you are in the selection list in the right portion of the menu tree Screen 2 Click to remove the selection Case Tab The Case Tab is where you enter all of the information at the level of individual cases In this tab you can
32. licked a popup window appears listing possible matches found in the terminology When a match is selected the terminology information will be displayed for that item To import information from the terminology into the knowledge base select the appropriate term and click OK 27 Lookup in Terminology PERIVASCULAR DERMATITIS Perivascular Eczema 00013595 Dermatitis Disease or Syndrome Eczema lr Definition pruritic papulovesicular dermatitis occurring as a reaction to many endogenous and exogenous agents synonyms ECZEMATOUS SKIN LESIONS Eczema disorders Eczema NOS eczematous dermatitis Eczerna discoid or NOS disorder Eczema HOS disorder Eczematous dermatitis Dermatitis Eczematous eczema Dermatitides Eczematous Eczema Eczema HOS ECZEMATOUS DERMATITIS Eczermatous Dermatitides Unclassifiable eczema disorder Eczema discoid or H05 Eczematous Dermatitis Eezemas Unclassifiable eczema Eczema Ambiguous disorder DERMATITIS ECZEMATOID ECZEMA Eczemnatous dermatitis HOS i Eczematoid dermatitis sources CST COSTAR MSH MEDLINEPLUS LECH CSP MTHICDY SNOMEDCT DXF NCI 40D OWIEWKI Relations view related concepts Creating a Worksheet Some clinical information may be added to a report using the worksheet button Using this button information can be added by selecting the appropriate radio buttons rather than typing itin To
33. ll be highlighted yellow Preview Cases Cases can be previewed in the Validation Tab When you double click a case a popup window will appear containing a preview of the digital slides and the pathology report assigned to that case during case authoring You can open the case using the Go To option described below AUTHORING NOTE Cases are colored based on the Case Status assigned from the Case Tab Cases in red are Incomplete cases Cases in blue are Completed cases Cases in green are Tested cases Right Click Menu Options Several options are available when you right click a finding diagnosis or case in the Validation Tab 37 Glossary The glossary option will display the definition of the selected finding or diagnosis For cases the glossary will display the difficulty of the case and whether the case is ready to use To view glossary information for an item right click the item and select the Glossary option Bookmark Unbookmark Bookmarks can be set to help with verification When a bookmark is set any items linked with that item will be highlighted green For example if a bookmark is set for a particular finding all diagnoses and cases containing that finding will be marked If a diagnosis is bookmarked all findings that diagnosis contains and cases with that diagnosis will be marked To set a bookmark right click the item and select the Bookmark option A bookmark that has been set can be removed by right clicking th
34. ll simply move the shape to that new tag Copying shapes will duplicate the shape which can then be pasted under a different tag To copy a shape 1 Right click the shape and select Duplicate Shape or select the shape and select Copy from the Edit menu To paste a shape 1 Select the tag that you want to paste to and select Paste from the Edit menu To cut a shape 1 Select the shape that you want to cut and select Cut from the Edit menu Taking Example Pictures from a Digital Slide You have the ability to capture a region of a digital slide to be saved as an example picture of any Knowledge Base concept To take a screenshot 1 Click the Ei button 2 Select the portion of the screen you want to take a screenshot of by holding down the left mouse button and dragging the mouse A shaded box will indicate what region is selected 17 3 Navigate to the folder where you want the screenshot to be saved 4 Type in a file name for the screenshot to be saved as in the File Name box 5 Click Save Tags Tags can be created to group annotations together to keep them organized and to simply linking annotations with concepts For example if you have drawn a lot of shapes marking the area of a lymphocytic infiltrate you might want to create a tag called lymphocytes and put all of the lymphocyte shapes under this tag Create a Tag To create a single tag 1 Click the button in the shapes tab choose Add Tag from the C
35. load digital slides add clinical report information annotate the digital image and link annotations with knowledge base concepts This entire process is referred to as case authoring DomainBuilder File Edit Case Annotations Tools Options Help D Case amp Knowledge Validation te gege D E Finaings Repon er estore FINAL DIAGNOSIS GROSS DESCRIPTION Knowledge Base Concepts Panel MICROSCOPIC wy COMMENT Clinical Report Panel Digital Slide Viewer Panel m Tele el eI slides shapes E domain http slidetutor upme edufcurriculum fowl skin PIT T PerivascularDermatitis owl case NEWW CASE user authenticated as kayse from PITT Case Maintenance When the Case Tab opens it opens a new case Previously saved cases can be opened and cases can be imported and exported Creating a New Case To create a new Case 1 Click the LA button OR select New from the File menu Opening a Case To open a previously saved case 1 Click the button OR select Open from the File menu 2 Select the case you want to open by clicking it You can filter cases by selecting a diagnosis When a case is selected its diagnosis is highlighted if available anda preview of the report is shown You can also search for a case by the case name by typing in the Search field 3 Click OK
36. n is entirely submitted in cassette i MICROSCOPIC MARGIN INDETERMINATE pT Zb pMa pa GROSS DESCRIPTION Received in formalin and labeled lesion the specimen consists of one small ellipse measuring 0 8 x 0 3 0 3 cm There is a central pigmented lesion with raised center The specimen is entirely submitted in cassette A MICROSCOPIC Cut Copy Paste in the Report Like a word processor you can cut copy and paste text To cut or copy text 1 Highlight the text you wish to cut or copy using your mouse 2 Right click your mouse and select cut or copy To paste text 1 Move your cursor to the location you wish to paste text 2 Right click your mouse and select paste You may also use the standard keyboard shortcuts to cut copy and paste text Spelling Suggestions A spell checker is available to provide spelling suggestions To spell check the report AE 1 Click the v button 2 For each misspelled word select the correct spelling from the suggestions provided and click Change Using a Worksheet to Input Clinical Information Some clinical information may be added to a report using the worksheet button Using this button information can be added by selecting the appropriate radio buttons rather than typing it in To create a worksheet of concepts please see the creating a worksheet section To use a worksheet SS 1 Click the H button 2 If there are multiple worksheets available
37. n that diagnosis These options are performed using the NO OR and AND options To add rules for findings 1 Highlight the appropriate finding cell s by clicking and dragging your mouse 2 Click the appropriate rule button OR right click and choose the appropriate option Adding Multiple Patterns of a Diagnosis Sometimes a diagnosis can present itself with multiple visualized patterns In order to create multiple patterns for a given diagnosis make sure the diagnosis is added to the panel and then select the diagnosis name highlighted in yellow and click the OR button Another column will be added to the panel with the same diagnosis which indicates that this disease has two different patterns of findings associated with it Cut Copy Paste Findings Findings can also be linked to a diagnosis using the cut copy paste and delete options Below is a table listing each option a picture of the button used for that option and the keyboard shortcut The keyboard shortcuts for cut copy and paste are the standard keyboard shortcuts for these options Option Button Shortcut Cut E Ctrl X Copy ig Ctrl C Paste Ctrl V Delete Delete Align Findings Findings can be aligned to make comparing findings across diseases easier To align Align Findings findings click the possible button Findings will then be aligned as much as 31 Import Findings from Spreadsheet Findings can be automatically created and linke
38. nformation When a concept is selected in the hierarchy information for that concept can be added in the panel on the right hand side of the screen A definition can be added as well as synonyms and example pictures Name hyperkeratosis Import from Terminology WA thickened cornified layer of an epithelium usua lly an epidermis Surface and infundibula buts ometimes the Upper part of an eccrine duct and Hheoretically an apocrine duct Example Picture 26 Manually Adding Definitions and Synonyms It is important for definitions and synonyms of concepts to be included in the knowledge base To add a definition 1 Select the appropriate concept in the hierarchy by left clicking it 2 Click the definition textbox to place your text cursor 3 Type in the definition To add synonyms 1 Select the appropriate concept in the hierarchy by left clicking it 2 If there aren t any empty rows in the synonyms table click the c button to adda row 3 Click the first empty synonym textbox to place your text cursor 4 Type in the synonym You can move your cursor to other synonym textboxes by using your mouse like in step 2 above using the Tab or Enter keys on your Keyboard or using the up and down arrows on your Keyboard Importing Definitions and Synonyms from the Terminology Definitions and synonyms can also be imported from the terminology by clicking the button When this button is c
39. notation see the Linking Annotations with Knowledge Base Concepts section below Case Concept Properties interface reaction Assert Concept in Case _ Mark as Explicitly Absent Concept in Case Feature Prime Example in Case aan All Locations where Case Concept can be observed A Arrow 29 Polygond Polygon Polygons Polygon3 Polygon24 Polygon 1 Polygoni9 Polygont7 Polygonts Polygon13 Polygoni1 Polygont All Recommendations Advice associated with this concept 20 AUTHORING NOTE Using the concept authored above the ITS provides a hint using the Prime Example annotation to show the student what a lymphocyte looks like A m WW This is an example of lymphocytes more g Previous 5 6 Next gt Clear Linking Annotations with Knowledge Base Concepts Once annotations have been added to a case they should be linked with knowledge base concepts to establish what each shape s purpose is Each shape can be used for multiple concepts however each shape must be linked with at least one concept Linking can be done in numerous ways e Drag the shape or tag in the Shapes list up to the appropriate concept e Drag the concept to the appropriate shape or tag in the Shapes list e Right click the shape or tag and choose Link Choose the appropriate concept from the popup that appears e Right click the concept and choose Link Choos
40. onse AP 343 AP349 AP 342 AP 358 AP 359 AP 36 j j j vests of melanocytes in epidermis above scar A AP 368 AP 3 KEERA OA O LE Et of melanocytes in epidermis above scar Se Mee ea neurotization of melanocytes nodular lesion configuration ovoid nests of melanocytes in epidermis pagetoid spread AP 379 AP381 MES v u inflammantarni i Ee ANEN n natinant ann araatar than EA nariadnowval nralifaratinn nf malannamtaoac ninrmanntatinn EENS 387 AP 388 AP Diagnosis AP 392 AP 399 S AP 406 AP 407 AP 412 AP 413 AP 420 AP 421 ACRAL LENTIGINOUS MALIGNANT MELANOMA ATYPICAL CELLULAR BLUE NEVUS ATYPICAL MELANOCYTIC LESION ATYPICAL MELANOCYTIC NEVUS ATYPICAL NEVYUS OF GENITAL SKIN ATYPICAL SPITZNEVUS BALLOON CELL NEYUS BECKERS MELANOSIS BENIGN MELANOCYTIC LESION BLUENEVUS CAFE AU LAITMACULE CELLULAR BLUE NEVUS AP 424 AP 426 COMMON BLUE NEVUS Seidizieldgtagdclleif d zfidieedagiedizaifle S AP 431 AP 432 COMPOUND ATYPICAL NEVUS OF GENITAL SKIN COMPOUND ATYPICAL SPITZ NEVUS COMPOUND BALLOON CELL NEVUS AP 437 AP 438 COMPOUND CONGENITAL MELANOCYTIC NEVUS COMPOUND DESMOPLASTIC SPITZ NEVUS AP 444 AP 446 am d dc AM do domain httpWslidetutor upre edu curriculum owl skin PITT Melanocytic owl user not authenticated from PITT Search A search tool is available at the top of the screen to make finding particular items easier Simply type in the word or string you wish to search for Any items containing the search string wi
41. ort all of the concepts in the spreadsheet 6 Once the tool is finished importing the concepts you can click on the Hierarchy Builder tab to find all of the newly created concepts The concepts are not automatically created in a hierarchy from this import process All of the diagnoses are simply added to the DIAGNOSIS class and all findings are added to the DIAGNOSITC FINDINGS class In the Hierarchy Tab it is up to the user to create the proper hierarchy from the added concepts or use the button to organize the hierarchy automatically Find Replace Findings Inside all Diagnostic Rules Sometimes it may be desirable to replace all occurrences of one finding from all diagnostic rules with another or remove it all together Often times this happens 32 when two findings are merged into a single finding due to a typo or new information from a source To find replace findings inside all diagnostic rule 5 Click on the S button or Find Replace Finding from the Builder menu 6 Click the button next to Search for Finding field to add a finding to search for 7 Click the button next to Replace with Finding field to add a finding to replace it with 8 Click Find to open all diagnostic rules that contain the finding you are searching for OR click replace to perform a replacement operation in all rules that the finding is located in Below is a screen shot for the Find Replace function Find Replace Findings Search for Find
42. s within the Knowledge Base and have those concepts populated by clicking the ei button in the appropriate column Diagnosis Findings Report Clinical and or Ancillary AUTHORING NOTE For example if you know that the diagnosis is Bullous Pemphigoid you can utilize the get findings button in the Findings column to look up all of the appropriate findings for Bullous Pemphigoid in the Knowledge Base Conversely if you have a set of findings X Y and Z you can infer the possible diagnoses for that set of findings by clicking the get diagnoses button in the Diagnosis column Loading Digital Slides To load digital slides 1 Click the P button in the slides portion of the screen lower right hand side of the screen select Add Slide from the Case menu or Ae click the button in the center of the digital slide viewer panel 2 Select a location from the drop down menu The location is the registered institution that hosts the digital slide images 3 Browse for an appropriate digital slide keeping in mind that some slides can be organized within sub folders You can search for slides in the currently opened folder by typing text into the search field 12 Open Slide Image Location E Image List Image Preview FLIP H6FxID UPENN archive SH bladder breast colon cytology dicom dinosaurs qynecologicalBreast lowerGlTract pancreas T we en n 2 Search AUTHORI
43. the report 2 Right click the highlighted text 3 Choose Suggest Term from the drop down menu 4 Select the existing concept from the tree The highlighted text from the report will become a synonym of the existing concept 5 Click OK If you would like to create a new concept in the Knowledge Base from a term in the pathology report 1 Highlight the concept in the report that you would like to add to the Knowledge Base 2 Right click on the concept and click on Suggest Term 3 Select the parent concept in which you would like the new term to be created under If there is no parent concept that fits you can create a new concept by clicking ie 4 Click OK Adding Removing Knowledge Base Concepts to the Case In addition to pulling knowledge base concepts from a processed report knowledge base concepts can also be added and removed manually using the rr and 11 buttons for the appropriate concept type Diagnosis Findings Report Clinical or Ancillary To manually add knowledge base concepts 1 Click the button for whichever concept type you wish to add diagnosis finding or prognosis 2 Select the desired item s from the menu tree that appears To remove knowledge base concepts 1 Click the item you wish to delete to select it 2 Click the appropriate button for whichever concept type you are removing Getting Knowledge Base Concepts for a Case You can have DomainBuilder look for missing concept
44. to the C aSe s sssssussnssnnnnnnnnunnunnnnnnnnnnnnnnnnnna 11 Getting Knowledge Base Concepts for a Case ssssusussssususunnunununnununnnnununnnnununnnnunnnnnnnnannnnnnnnnnnn 12 EGading Distal Eege 12 V VSZIgIOAUTCIKU TEEN 13 More eat OL SN E 13 eier oy gO E 13 Refresh Digital Slide E 14 eA E OV A AE A A E A E 14 EA ett e 14 ING CERRY WAN DE SCS ass as ceca scenes csc nev seca a Eaa exevenetafeuepesteraneascieeenes 14 Expand Digital Slide Area ccssssssssseeseessesseeseessneneeseeeseseessneseesseesaeseneneseneneseessneseesseeneeesnenaess 16 Annotating Digital KE 16 PUL CIT WAM NA aaa a E a 17 URE Copy Paste SUA erer eege 17 Taking Example Pictures from a Digital Slide sssussssnnununnnnununnnnununnnnununnnnununnnnunnnnnnunnnnnnnnnna 17 ETC 18 Created TAS curnea E a Aaaa aa a 18 DEL EE 18 Organizing Annotations with WE 18 Case Authoring for SlideTutor I S s sssussssnusunnnnununnnnununnunununnunununnununnnnununnnnunnnnnnnnunnnnnnannnnnnnn nnna 19 Locations eege EE 19 Linking Annotations with Knowledge Base Concepts sssssussssussusunnununnunnnnunnununnunnnnunnnnnnnnnnne 21 Case Concept Properties eege 21 Viewing Case Concept dee e 22 Modifying Linked Annotations Using Case Concept Properties EEN 22 Ewe 22 Validating Knowledge Base Concepts fOr a Case ssssssssssususunnunununnnnununnununnnnununnnnnnunnnnnnnnnnnnnnn 22 Adding Additional Pathologies to the Case ssssssussususnununnunnnnunnnnunnununnunnnn
45. ts simply type the parent concept first and then in the next line insert a tab before the child concept For example if you wanted to create the following hierarchy under MALIGNANT E ER You would insert the following into the popup window Create New Concepts Enter a List of Concepts 1 Malignant Blue Nevus 2 Malignant Melanoma J Acral Lentiginous Malignant Melanoma Desmoplastic Malignant Melanoma In Situ and Invasive Malignant Melanoma Invasive Malignant Melanoma Malignant Melanoma In Situ HINT enter each concept on a new line use tabs to indicate hierarchy 4 Click OK Cut Copy Paste Delete Concept Options In addition to adding new concepts changes can be made to the knowledge base hierarchy using the cut copy paste and delete options Below is a table listing each option a picture of the button used for that option and the keyboard shortcut The keyboard shortcuts for cut copy and paste are the standard keyboard shortcuts for these options Option Button Shortcut Cut E Ctrl X Copy Ctrl C 25 Paste Ctrl V Delete Delete These options are also available when you right click a concept Information that is cut or copied is displayed in the clipboard popup box displayed in the lower left hand area of the screen to allow easy viewing of this material When the delete option is selected a confirmation box appears asking if you want to delete the selected item Adding Concept I
46. unnnnunnnnnnnnnnnnnnnnnnnnnnnnnn 22 Creating and Deleting Additional Pathologies een 23 Marking Unrelated Diagnoses with Respective Pathologies ccssssessesessssssssseseseseseseens 23 Viewing Different Pathologie csssssssesseseeseeseeseesseseeseesseeseeseeseeseeseeseesensseeseesenesoesenseneas 23 Case ENT E 23 FO WS CC Ta E 24 Hi rarchy Builder VAD sive cecestecschiececcessetasiecencessecyncuescbt iegecnvactzcceadeetevenesnibeevieat aaie 24 EIERE DEE 24 Cut Copy Paste Delete Concept OptionS s ss sssssresrrssrssnesrrsrrssnssnrnnresnssneonnnnnnsnnnnnnnnnnnnnnnonnennnnnnna 25 Adding Concept MIormation sssaaa aea aaa aN Aaaa a Na i 26 Manually Adding Definitions and Synonym 27 Importing Definitions and Synonyms from the Terminology Ee 27 Diagnosis Btn TaD sraa ice cdavieiens 29 Adding TEE EES EE 30 Adding Findings to HEES 30 leier attert 31 Adding Multiple Patterns Of a Diagnosis s sssussssusussnnunununnununnnnununnnnununnnnununnnnnnunnnnnnunnnnnnnnnnnnnnn 31 Cut Copy Paste Anere Eege 31 Aun ET 31 Import Findings from Spreadsheet vvciisicccciscssestsssscsncsisvedecasucscessasensnctssenvedocesassciusnessersersecsuceees 32 Find Replace Findings Inside all Diagnostic Rules s ssssssssussnnunnnnunnununnunnnnunnnnunnunnnnunnnnnnnnnnne 32 Report B ilder tee 33 Creating a New Template nenisnnnniianienn n EES 34 Delen a Ten 34 R p rtaple ITEMS airea a 34 Adding Reportable em E ER Delenne Reportable e ER Reorder Reportaple Hela
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