Chart Review
User Manual
Version 1.0
Oct 2014
Department of Veterans Affairs (VA)
VINCI
Revision History
Table 1. Documentation revision history
Date
Revision
Description
Author
10/20/2014
1.0
· Initial version
· Brad Adams
REF: This is an initial version of the user manual
Contents
User Manual.................................................................................................................................. i
Figures........................................................................................................................................ v
Tables...................................................................................................................................... viii
What is Chart Review?............................................................................................................. xi
How to Use this Manual.......................................................................................................... xii
Intended Audience.................................................................................................................. xii
Legal Requirements................................................................................................................ xii
Disclaimers.............................................................................................................................. xii
Documentation Conventions................................................................................................ xiii
Assumptions........................................................................................................................... xiii
References / Online Demo.................................................................................................... xiii
1 Introduction.......................................................................................................................... 1
1.1 System Architecture Must-Knows.................................................................................. 1
1.2 System Integration Must-Knows.................................................................................... 2
1.3 The Chart Review Home Page......................................................................................... 3
1.4 Setting up your Browser for Chart Review.................................................................... 6
1.4.1 General Setup...................................................................................................................................................... 6
1.4.2 Single Sign On (SSO) Setup............................................................................................................................ 6
2 Admin...................................................................................................................................... 7
2.1 Overview............................................................................................................................ 7
2.2 Project Clinical Element Configurations (User/Admin).............................................. 8
2.3 Projects (User/Admin).................................................................................................. 22
2.4 Reports (User/Admin)................................................................................................... 36
2.5 Schemas (User/Admin).................................................................................................. 49
2.6 Failed Jobs (Admin only)............................................................................................... 61
2.7 Process Templates (Admin only)................................................................................. 62
2.8 Tools and Utilities (Admin only).................................................................................. 63
2.9 Users (Admin only)........................................................................................................ 65
2.10 About (Admin only)..................................................................................................... 69
2.11 Log Level (Admin only)................................................................................................ 71
2.12 Performance Monitoring (Admin only)..................................................................... 72
3 Chart Review...................................................................................................................... 75
3.1 Overview......................................................................................................................... 75
3.2 Quick-Start...................................................................................................................... 76
3.3 Initiating a Chart Review............................................................................................... 76
3.4 Layout Options............................................................................................................... 78
3.4.1 Two Column Mode........................................................................................................................................ 78
3.4.2 Variable Height Views.................................................................................................................................. 80
3.4.3 View Detail Docking/Hiding Options.................................................................................................... 81
3.4.4 Optional Column Inclusion........................................................................................................................ 82
3.4.5 List Sorting........................................................................................................................................................ 84
3.4.6 List Grouping.................................................................................................................................................... 84
3.4.7 Variable Column Order and Size.............................................................................................................. 86
3.4.8 Collapsible Views............................................................................................................................................ 87
3.4.9 Delete View....................................................................................................................................................... 88
3.4.10 Add View......................................................................................................................................................... 89
3.4.11 Multiple Instances of the Same View (comparison) and the Auto-select Toggle............ 90
3.4.12 Closable Annotation Panel....................................................................................................................... 91
3.5 Workflow Support......................................................................................................... 92
3.5.1 View In New Tab............................................................................................................................................ 92
3.5.2 Marking Records As Done........................................................................................................................... 94
3.5.3 Optional Text Wrapping.............................................................................................................................. 94
3.5.4 Description Hiding......................................................................................................................................... 96
3.6 Annotation Workflow.................................................................................................... 97
3.7 Annotation Schema........................................................................................................ 98
3.8 Annotation of Clinical Element Text............................................................................ 99
3.9 Annotation of Whole Context Clinical Element (i.e. Note, Lab).............................. 101
3.10 Annotation of Principal Clinical Element (i.e. Patient)......................................... 102
3.11 The Annotation List................................................................................................... 103
3.12 Editing Annotation Attributes................................................................................. 105
Figures and Tables
Figures
Figure 1: Chart Review Data Sources................................................................................................ 2
Figure 2: Chart Review Integrations.................................................................................................. 3
Figure 3: Chart Review Home Page.................................................................................................. 4
Figure 4. Admin – Project Clinical Element Configurations.............................................................. 8
Figure 5. Admin – Show Clinical Element Configuration – General Configuration........................ 10
Figure 6. Admin – Show Clinical Element Configuration – General Configuration – Edit.............. 12
Figure 7. Admin – Show Clinical Element Configuration – Columns............................................. 14
Figure 8. Admin – Show Clinical Element Configuration – Content Template................................ 15
Figure 9. Admin – Create Clinical Element Configuration – Step 1 – Define Test Connection and Queries 16
Figure 10. Admin – Create Clinical Element Configuration – Step 2 – Data Set Column Definition & Other Metadata................................................................................................................................ 18
Figure 11. Admin – Create Clinical Element Configuration – Step 3 – Preview Output.................. 20
Figure 12. Admin – Create Clinical Element Configuration – Step 4 – Name and Description....... 21
Figure 13. Admin – Project List...................................................................................................... 22
Figure 14. Admin – Project – Show – General Configuration......................................................... 23
Figure 15. Admin – Project – Show – Documents.......................................................................... 25
Figure 16. Admin – Project – Show – Project Users........................................................................ 26
Figure 17. Admin – Project – Show – Processes............................................................................. 27
Figure 18. Admin – Project – Edit – General Configuration............................................................ 28
Figure 19. Admin – Project – Edit - Project Users........................................................................... 29
Figure 20. Admin – Project – Add Process – Step 1 – Choose the Process to Add.......................... 30
Figure 21. Admin – Project – Add Process – Step 2 – Process Parameters...................................... 31
Figure 22. Admin – Project – Add Process – Step 3 – Users and Clinical Elements In This Process 34
Figure 23. Admin – Project – Run SQL Query................................................................................ 35
Figure 24. Admin – Chose Project and Processes For Reports........................................................ 36
Figure 25. Admin – Reports............................................................................................................ 37
Figure 26. Admin – Report – Annotations Per Annotator Detail..................................................... 38
Figure 27. Admin – Report – Annotations Per Annotator Detail – Clinical Element....................... 40
Figure 28. Admin – Report – How Many Annotations By Type..................................................... 41
Figure 29. Admin – Report – How Many Annotations By Annotator And Type............................. 42
Figure 30. Admin – Report – Patients Per Annotator and Process................................................... 43
Figure 31. Admin – Report – Patients Per Annotator And Process DETAIL................................... 44
Figure 32. Admin – Report – Patients Reviewed More Than Once................................................. 46
Figure 33. Admin – Report – Inter-Annotator Agreement – Original Report................................... 47
Figure 34. Admin – Report – Inter-Annotator Agreement – New Report........................................ 48
Figure 35. Admin – Schema List..................................................................................................... 49
Figure 36. Admin – Schema – General Configuration.................................................................... 51
Figure 37. Admin – Schema – Attributes........................................................................................ 52
Figure 38. Admin – Schema – Attribute – Create/Edit.................................................................... 53
Figure 39. Admin – Schema – Attribute – Create/Edit - Numeric.................................................... 54
Figure 40. Admin – Schema – Attribute – Create/Edit - Date.......................................................... 55
Figure 41. Admin – Schema – Attribute – Create/Edit - Option...................................................... 56
Figure 42. Admin – Schema – Attribute – Create/Edit - Option................................... - Create/Edit Option 57
Figure 43. Admin – Schema – Classifications................................................................................. 58
Figure 44. Admin – Schema – Classification – Create/Edit – General Configuration...................... 59
Figure 45. Admin – Schema – Classification – Create/Edit – Attributes.......................................... 60
Figure 46. Admin – Failed Jobs...................................................................................................... 61
Figure 47. Admin – Process Templates........................................................................................... 62
Figure 48. Admin - Tools and Utilities............................................................................................ 63
Figure 49. Admin - Tools and Utilities – API Docs......................................................................... 64
Figure 50. Admin - Users................................................................................................................ 65
Figure 51. Admin – Show User....................................................................................................... 66
Figure 52. Admin – Edit User......................................................................................................... 67
Figure 53. Admin - About............................................................................................................... 69
Figure 54. Admin - About – API Docs............................................................................................ 70
Figure 55. Admin - Log Level......................................................................................................... 71
Figure 56. Admin – Performance Monitoring – Top....................................................................... 72
Figure 57. Admin – Performance Monitoring - Bottom................................................................... 73
Figure 58. Chart Review................................................................................................................. 75
Figure 59. Chart Review – Initiating a Chart Review...................................................................... 77
Figure 60. Chart Review – Two Column Mode............................................................................... 79
Figure 61. Chart Review – Single Column Mode............................................................................ 79
Figure 62. Chart Review – Variable Height Views.......................................................................... 81
Figure 63. Chart Review – View Detail Docking/Hiding Options.................................................... 82
Figure 64. Chart Review – Optional Column Inclusion................................................................... 83
Figure 65. Chart Review – List Sorting........................................................................................... 84
Figure 66. Chart Review – List Grouping........................................................................................ 85
Figure 67. Chart Review – Variable Column Order and Size.......................................................... 86
Figure 68. Chart Review – Collapsible Views................................................................................. 87
Figure 69. Chart Review – Delete View.......................................................................................... 88
Figure 70. Chart Review – Add View............................................................................................. 89
Figure 71. Chart Review – Multiple Instances of the Same View (Comparison)............................. 90
Figure 72. Chart Review – Auto-select Toggle................................................................................ 91
Figure 73. Chart Review – Closable Annotation Panel.................................................................... 92
Figure 74. Chart Review – View in New Tab.................................................................................. 93
Figure 75. Chart Review – Marking Records As Done.................................................................... 94
Figure 76. Chart Review – Optional Text Wrapping....................................................................... 95
Figure 77. Chart Review – Description Hiding................................................................................ 96
Figure 78. Chart Review – Task Panel and Toolbar........................................................................ 97
Figure 79. Chart Review – Annotation Schema.............................................................................. 99
Figure 80. Chart Review – Annotation of Clinical Element Text.................................................. 100
Figure 81. Chart Review – Annotation of Whole Clinical Element............................................... 101
Figure 82. Chart Review – Annotation of Principal Clinical Element............................................ 102
Figure 83. Chart Review – Annotation List................................................................................... 104
Figure 84. Chart Review – Editing Annotation Attributes............................................................. 106
Tables
Table 1. Documentation revision history.......................................................................................... ii
Table 2: Chart Review Main Toolbar................................................................................................ 4
Table 3: Admin – Project Clinical Element Configuration List.......................................................... 8
Table 4: Admin – Show Clinical Element Configuration – General Configuration......................... 10
Table 5: Admin – Show Clinical Element Configuration – General Configuration - Edit................ 12
Table 6: Admin – Show Clinical Element Configuration – Columns.............................................. 14
Table 7: Admin – Show Clinical Element Configuration – Content Template................................. 15
Table 8: Admin – Create Clinical Element Configuration – Step 1 – Define Test Connection and Queries 16
Table 9: Admin – Create Clinical Element Configuration – Step 2 – Data Set Column Definition & Other Metadata................................................................................................................................ 18
Table 10: Admin – Create Clinical Element Configuration – Step 3 – Preview Output................... 20
Table 11: Admin – Create Clinical Element Configuration – Step 4 – Name and Description........ 21
Table 12: Admin – Show Project – General Configuration............................................................. 22
Table 13: Admin – Project – Show – General Configuration.......................................................... 23
Table 14: Admin – Project – Show – Documents........................................................................... 25
Table 15: Admin – Project – Show – Project Users......................................................................... 26
Table 16: Admin – Project – Show – Project Users......................................................................... 27
Table 17: Admin – Project – Edit – General Configuration............................................................. 28
Table 18: Admin – Project – Edit – Project Users........................................................................... 29
Table 19: Admin – Project – Add Process – Step 1 – Choose the Process to Add........................... 30
Table 20: Admin – Project – Add Process – Step 2 – Process Parameters....................................... 32
Table 21: Admin – Project – Add Process – Step 3 – Users and Clinical Elements In This Process 34
Table 22: Admin – Project – Run SQL Query................................................................................. 35
Table 23: Admin – Chose Project and Processes For Reports......................................................... 36
Table 24: Admin – Reports............................................................................................................. 37
Table 25: Admin – Report – Annotations Per Annotator Detail...................................................... 38
Table 26: Admin – Annotations Per Annotator Detail – Clinical Element....................................... 40
Table 27: Admin – Report – How Many Annotations By Type...................................................... 41
Table 28: Admin – Report – How Many Annotations By Annotator And Type.............................. 42
Table 29: Admin – Report – Patients Per Annotator and Process.................................................... 43
Table 30: Admin – Report – Patients Per Annotator and Process DETAIL..................................... 45
Table 31: Admin – Report – Patients Reviewed More Than Once.................................................. 46
Table 32: Admin – Report – Inter-Annotator Agreement – Original Report.................................... 47
Table 33: Admin – Report – Inter-Annotator Agreement – New Report......................................... 48
Table 34: Admin – Schema List...................................................................................................... 49
Table 35: Admin – Schema – General Configuration..................................................................... 51
Table 36: Admin – Schema – Attributes......................................................................................... 52
Table 37: Admin – Schema – Attribute – Create/Edit..................................................................... 53
Table 38: Admin – Schema – Attribute – Create/Edit - Numeric..................................................... 54
Table 39: Admin – Schema – Attribute – Create/Edit - Date........................................................... 55
Table 40: Admin – Schema – Attribute – Create/Edit - Option....................................................... 56
Table 41: Admin – Schema – Attribute – Create/Edit - Option....................................................... 57
Table 42: Admin – Schema – Classifications.................................................................................. 58
Table 43: Admin – Schema – Classification – Create/Edit – General Configuration....................... 59
Table 44: Admin – Schema – Classification – Create/Edit - Attributes........................................... 60
Table 45: Admin – Process Templates............................................................................................ 62
Table 46: Admin – Tools and Utilities............................................................................................ 63
Table 47: Admin – Tools and Utilities – API Docs......................................................................... 64
Table 48: Admin – Users................................................................................................................ 65
Table 49: Admin – Show User........................................................................................................ 66
Table 50: Admin – Show User........................................................................................................ 68
Table 51: Admin – About............................................................................................................... 69
Table 52: Admin – About – API Docs............................................................................................ 70
Table 53: Admin – Log Level......................................................................................................... 71
Table 54: Admin – Performance Monitoring.................................................................................. 73
Table 55: Chart Review – Initiating a Chart Review....................................................................... 77
Table 56: Chart Review – Two Column Mode................................................................................ 80
Table 57: Chart Review – Variable Height Views........................................................................... 81
Table 58: Chart Review – Variable Height Views........................................................................... 82
Table 59: Chart Review – Optional Column Inclusion.................................................................... 83
Table 60: Chart Review – List Sorting............................................................................................ 84
Table 61: Chart Review – List Grouping......................................................................................... 85
Table 62: Chart Review – Variable Column Order and Size........................................................... 86
Table 63: Chart Review – Collapsible Views.................................................................................. 87
Table 64: Chart Review – Delete Views......................................................................................... 88
Table 65: Chart Review – Add View.............................................................................................. 89
Table 66: Chart Review – Closable Annotation Panel..................................................................... 92
Table 67: Chart Review – View In New Tab.................................................................................. 93
Table 68: Chart Review – Marking records as Done....................................................................... 94
Table 69: Chart Review – Optional Text Wrapping........................................................................ 95
Table 70: Chart Review – Description Hiding................................................................................. 97
Table 71: Chart Review – Task Panel and Toolbar......................................................................... 97
Table 72: Chart Review – Annotation Schema............................................................................... 99
Table 73: Chart Review – Annotation of Clinical Element Text................................................... 100
Table 74: Chart Review – Annotation of Clinical Element Text................................................... 101
Table 75: Chart Review – Annotation List.................................................................................... 104
Table 76: Chart Review – Editing Annotation Attributes.............................................................. 107
Orientation
What is Chart Review?
Chart Review is a manual, multi-level annotation tool. Its configurable medical record interface, allows annotation at any level of the record (i.e. note part or whole, lab value part or whole, patient part or whole, etc.) in a configurable, multi-annotator workflow. Annotating within the context of the whole patient chart allows reviewers to follow a more natural clinical process of finding and aggregating patient information, while still supporting powerful annotation capabilities.
Chart Review displays all aspects of a medical record, from any database environment. Though Chart Review was built to specifically allow its use in the VINCI research environment (taking into account the VINCI project database configuration and policies), it can be used in any database environment where medical records may be kept. Access to the data layer is configurable in the UI, allowing the tool to access any database environment, with any database schema definition.
The tool also allows configuration of annotation workflow processes which make annotation tasks available to multiple annotators using the application simultaneously. Annotations are saved and viewable in downstream tasks and processes, whether inside or outside of the system. This tool can share inputs and outputs with other NLP processes and annotation tools through standard definitions and standard access of clinical elements (i.e. documents, records) and annotations. In addition, annotation statistics are provided for workflow analysis.
Chart Review provides features such as:
· Definition of clinical elements (notes, labs, radiology, problems, meds, etc.)
· Definition of available process types (single step, multi-step, graph, etc.)
· Definition of projects (users, workflow processes, tasks, views, cohorts, and mapping to the data source, etc.)
· Reports (workflow process, annotation activity, etc.)
· User definition
· Project workflow maintenance and trouble shooting tools and utilities
· System performance monitoring
· System help
The features of Chart Review listed above may only be accessible to users with certain roles and privileges. A typical annotator, for example, may not have access to the project definition features that are available to a project coordinator.
Chart Review is a public domain software package that is developed and maintained by the Department of Veterans Affairs. It is widely used in the VA VINCI research environment as well as in university settings. It may be used in commercial settings in the future.
How to Use this Manual
The Chart Review User Manual is designed to provide you, the Chart Review user, with screen-by-screen "how to" information on the usage of Chart Review.
This manual is divided into two main sections: Chart Review System and Project Administration, and Reviewing a Chart. The manual will provide explanations of each screen and of all user interface options within the context of an easy to understand demonstration data scenario.
NOTE: This document is available in Microsoft Word (.doc), Adobe Acrobat Portable Document Format (PDF), and Hypertext Markup Language (HTML) format as online-help.
Intended Audience
This manual will distinguish features that are available to project administrators from those available to other project users (i.e. annotators).
Legal Requirements
There are no special legal requirements involved in the use of Chart Review.
Disclaimers
This manual provides an overall explanation of Chart Review and the functionality contained in Chart Review 1.0; however, no attempt is made to explain how the reader may access the VINCI environment or procure and view data within that environment. We suggest contacting VINCI management directly from the VA network at vaww.vinci.med.va.gov.
DISCLAIMER: The appearance of external hyperlink references in this manual does not constitute endorsement by the Department of Veterans Affairs (VA) of this Website or the information, products, or services contained therein. The VA does not exercise any editorial control over the information you may find at these locations. Such links are provided and are consistent with the stated purpose of the VA.
Documentation Conventions
This manual uses several methods to highlight different aspects of the material:
· Various symbols are used throughout the documentation to alert the reader to special information. Table gives a description of each of these symbols:
Table 1. Documentation symbol descriptions
Symbol
NOTE/REF: Used to inform the reader of general information including references to additional reading material.
CAUTION/RECOMMENDATION/DISCLAIMER: Used to caution the reader to take special notice of critical information.
Assumptions
This manual is written with the assumption that the reader is familiar with the following:
· SQL – there will be many references to SQL code in setting up a project’s mapping to a data source.
References / Online Demo
Readers who wish to learn more about Chart Review should consult the following documents:
· Chart Review Release Notes (TBD)
· Chart Review Installation Guide (TBD)
· Chart Review Technical Manual (TBD)
· ChartReview User Manual (this manual; PDF and HTML format)
· Chart Review Developer’s Guide (TBD)
ONLINE DEMO: A demo of Chart Review and its online help is available on the VA intranet at: http://vhacdwweb03:8080/chart-review/ Using a Fire Fox (ver > 30) browser, open Chart Review and, after logging in as admin/admin (project administrator features) or project1/project1 (annotator features), access the help link at the top of the page.
In defining annotation project workflow processes, it benefits the user to understand some basic concepts about the architecture of data sources in Chart Review. First, Chart Review stores information that is central to the application and shared by all projects, such as user profiles, the list of projects in a central database. This information is assumed to not require special security maintained by an outside security manager.
Next, Electronic Health Record information is usually stored in a database that is securely maintained by an outside security manager. In the case of VINCI data, for example, the VINCI data management team places the data in project specific databases and individual end users are given permissions to those databases and tables. When a user logs into Chart Review, his permissions are passed on to the database system when he tries to access project specific information. He will only be able to see EHR and project specific data, such as annotation process tasks and annotations in project databases for which he has been given permission by the data management team. In defining and annotation project workflow process in the Chart Review tool, a project coordinator will need to specify database connectivity information and provide SQL queries to access EHR information. Please note that errors in the definition of these configuration elements may be the result of database access permissions that are not controlled by the Chart Review tool.
Finally, Chart Review stores other annotation project information that is project specific in the project database along with the EHR information, including clinical element definitions, annotation schemas, workflow process tasks, as well as annotations. These data elements may contain secure information if, for example, a clinical element configuration (the SQL used to query/transform EHR data into data viewed in Chart Review) contained a list of patient ids as a criteria.
Figure 1: Chart Review Data Sources
In defining annotation project workflow processes, it benefits the user to understand some basic concepts about the way other systems can be integrated with Chart Review. For example, an automated annotation system, like one based on the LEO or SIMON frameworks, may be used to automatically generate symptoms or other pre-annotations that can then be seen by a manual annotator in the Chart Review tool to help them with their annotation tasks. The LEO and SIMON frameworks allow these tools to share clinical element configurations and schemas, and to generate pre-annotations that can be seen in Chart Review. The automated annotator may first pull clinical element definitions from the project database. These elements allow the system to understand what a “document” that needs to be annotated looks like (i.e. its content and format). This document may be a traditional note, or it may be a lab, problem, medication list, patient demographic record, etc. It is important that both the automated annotation system and the Chart Review system agree on what a given clinical element looks like so that annotations created on that element by the one system can be seen correctly in the other system. Next, sharing schemas allows the automated annotator to generate annotations that relate to classifications and have class attributes and relationships that may then be understood and viewed in Chart Review. Process tasks could be utilized by both systems to sequence the pre-annotation task with the manual annotation task.
As another example of integration, there may be a validation tool that would take the manual annotations created in Chart Review and allow an analyst to do a quick validation of the given annotation in a validation tool like CHEX. Similar to an automated annotation tool, a validation tool would use the configuration information such as clinical element configurations, schemas, and process tasks as well as the manual annotations created in Chart Review to allow an analyst to validate the annotations and produce validation annotations, confirming the validity of the manual annotations. These validation annotations could subsequently be viewed in Chart Review.
Figure 2: Chart Review Integrations
The Chart Review home page is the main screen from which any user can access all admin features or the chart reviewing features of the tool. The tool bar at the top of the page gives access to the various parts of the application and can be found on every page of the application, allowing the user to jump from one part of the application to another.
Figure 3: Chart Review Home Page
This table lists the features that can be access from the main Chart Review toolbar:
Table 2: Chart Review Main Toolbar
Item/Action
Description/Result
ChartReview
Takes you to this home page again.
Home
Admin -> Clinical Element Configurations
Takes you to the pages that allow definition of the various chart information views that will be available to view and annotate during chart review, for example, labs, notes, radiology reports, problems, medications, etc.
Admin -> Projects
Takes you to the pages that allow definition of a project, its processes, tasks, and database mappings, etc.
Admin -> Reports
Takes you to the pages that allow perusal of analytical reports about various aspects of the projects, including task completion, annotations made, inter-annotator agreement, etc.
Admin -> Schemas
Takes you to the pages that allow definition of classifications, class attributes, and class relationships that will be available to annotate the chart with for a each annotation workflow process task.
Admin -> Failed Jobs
Takes you to a list of failed workflow processes.
Note that different annotators may be participating in different annotation workflows simultaneously.
Admin -> Processes
Takes you to the pages that allow upload and definition of process pre-defined process templates that may be used in creating process instances for a given project.
Admin -> Tools and Utilities
Takes you to the pages that provide tools and utilities to, for example, kill processes, or view API documentation.
Admin -> Users
Takes you to the pages that allow user definition and maintenance.
Admin -> About
Takes you to the pages that show information about the application, its version, structure, dependencies, and components.
Admin -> Log Level
Takes you to the pages that allow control over the various levels of system logging available.
Admin – Performance Monitoring
Takes you to the pages that show performance monitoring analytics about the Chart Review system itself.
Help
Takes you to the help pages.
Settings
Takes you to the pages that allow system settings, for example, changing the current user’s password.
Logout (username)
Logs you out and takes you to the login screen.
Switch User
Takes you to the pages that allow switching between users without changing your database connection permissions.
Chart Review us available on the Firefox browser only, version 30+.
Access to the server may take several seconds, or more, depending upon the underlying database schema and the queries defined in the project processes. Because of this, the browser java script timeout default needs to be set to infinity, to not timeout the scripts. This is done in the Firefox configuration screens by setting max_script_run to zero.
1) In the address area of Firefox, type the following:
About:config
2) In the search area, type the following:
Max_script_run
Double click on the value of this variable, and set it to zero.
See the User Guide for Single Sign On to setup single sign for the VINCI environment. Information in that document contains VA confidential environment information, so it is not include in this document.
The Admin pages in Chart Review allow a project administrator to set an annotation project, including: define clinical elements, annotation schemas, and annotation process templates and workflows. It also provides system administration functions such as user management, failure reports, database utilities, logging control and performance monitoring.
The Clinical Element Configuration item in the Admin drop down menu takes you to the pages that allow definition of the various chart information views that will be available to view and annotate during chart review, for example, labs, notes, radiology reports, problems, medications, etc. Chart Review gives complete control to a project administrator over defining what the clinical elements are, what data they contain, how they are mapped from a data source, and how they will be viewed during chart review. While these configurations belong to a give project, a user that has permissions to multiple projects is able to copy (not share) configurations between those projects, in the event that data sources and configurations are similar between projects.
Figure 4. Admin – Project Clinical Element Configurations
Table 3: Admin – Project Clinical Element Configuration List
New Clinical Element Configuration
Creates a new clinical element configuration and takes you to the clinical element configuration editor.
Project Clinical Element Configurations
This section contains all configurations that belong to this project.
Change
Allows you to change which project’s clinical element configurations are listed.
Name link
Sorts table by project clinical element configuration name.
Name
The name of each clinical element configuration owned by the specified project.
List item name
Shows the selected clinical element.
Description link
A brief description of the clinical element configuration.
Active link
Sorts table by project clinical element configuration active status.
Active
Indicates if the user can choose this configuration when defining a process. As configurations age, they will be “turned off”.
Edit
Edits the specified configuration.
Delete
Deletes the specified configuration.
Copy
Copies the specified configuration.
Export
Exports the specified configuration to JSON in a separate tab.
Clinical Element Configurations Available From Other Projects
This section contains all configurations that belong to projects that the user has access to.
The name of each clinical element configuration belonging to a project the user has access to.
Copy To Project
Copies the specified configuration into the current project.
Exports the specified configuration to a JSON in a separate tab.
Upload New Clinical Element Configuration
Allows the user upload of a configuration specified in a JSON file.
Browse
Find the file in the local browser’s file system.
Upload
Upload the configuration.
Figure 5. Admin – Show Clinical Element Configuration – General Configuration
Table 4: Admin – Show Clinical Element Configuration – General Configuration
Name of the configuration.
Simple description of the configuration.
Title Field
The database field that is the title of this configuration.
Description Field
The database field that is the description of this configuration.
Type
The type of this clinical element configuration. Summary is one record per primary clinical element (patient), list is multiple records per principal clinical element (patient).
All Elements By Patient Id Query
Queries all context clinical elements by the principal clinical element id (i.e the patient id). For example, this query could return all elements of this type that belong to a given patient (plus any other desired criteria).
This SQL queries a project database.
Single Element Query
Queries a single clinical element of this type. The goal of this query is to return a single record by specifying any criteria in the where clause that are needed to identify the record uniquely. The criteria may include the relationship to the principal clinical element (i.e. the patient), but does not have to. The record id alone could be the only criteria, in the most simple case.
Created By
The user that created the configuration.
Created Date
The date that the configuration was created.
Figure 6. Admin – Show Clinical Element Configuration – General Configuration – Edit
Table 5: Admin – Show Clinical Element Configuration – General Configuration - Edit
LIST – The clinical element view shows a list of clinical element items (like note documents), with a detail section that is displayed when an item is selected.
SUMMARY – The clinical element view shows only a summary of the clinical element item(s) (like an overview of a patient’s demographic information, or a graph of all labs through time).
Update
Saves the edits to the configuration.
Figure 7. Admin – Show Clinical Element Configuration – Columns
Table 6: Admin – Show Clinical Element Configuration – Columns
Column Name
The column name from the result set
Display Name
The name that will be presented as the name of the clinical element view during chart review.
Type Name
The database type for the column.
Key Field
Key fields in the database should be true. Others, false.
Exclude
Excluded fields are not visible in the item grid during chart review, but are used as part of the detail content template.
Figure 8. Admin – Show Clinical Element Configuration – Content Template
Table 7: Admin – Show Clinical Element Configuration – Content Template
Content Template
The content template is a definition of the format of the detail display of the selected clinical element item during chart review. Database fields are specified as ${field_name}. Other characters are displayed in the detail view as-is. Style can be added to the content by applying it to the template, including the database fields.
Figure 9. Admin – Create Clinical Element Configuration – Step 1 – Define Test Connection and Queries
Table 8: Admin – Create Clinical Element Configuration – Step 1 – Define Test Connection and Queries
Jdbc Driver
The jdbc driver that will be used to connect to the database.
Connection String
Standard jdbc database connection string (i.e. jdbc:mysql://localhost/chartreview?useUniode=yes&characterEncoding=UTF-8)
Jdbc Username/Password
Username and passw0rd to connect to the databse with. If using integrated authentication, these can be left blank.
All Elements by Patient Id Query
NOTE: Query All Elements by Patient Id query can be any query, but must follow these rules:
An example query might be:
select lab.lab_value, icd9.icd9_code, lab.lab_id from lab, icd9_code, patient where lab.lab_icd9 = icd9.icd9 and lab.patient_id = patient.patient_id and patient.patiend_id = ?
In the above example, lab.lab_id uniquely identifies the lab row for this clinical element.
NOTE: The columns and order MUST match that of the Query All Elements by Patient Id above exactly.
Example Patient Id
An example patient id for querying the database to get table metadata.
Next
Go to the next step in the Create Clinical Element Configuration wizard.
Figure 10. Admin – Create Clinical Element Configuration – Step 2 – Data Set Column Definition & Other Metadata
Table 9: Admin – Create Clinical Element Configuration – Step 2 – Data Set Column Definition & Other Metadata
Content Template Toggle
Yes if this configuration has a content template, No otherwise.
A LIST type configuration usually has a content template that displays the detail of a clinical element record in a formatted document way. There may be cases where a LIST type configuration may just be displayed in a list, with no detailed, document view if a document view does not add any information that would not be seen in the columns of the clinical element grid in Chart Review, and if annotation never needed to occur on text within the detail. If there were no content template provided, an entire clinical element record could still be annotated as a whole within Chart Review.
A SUMMARY type configuration must have a content template. This template would display the only view available of the clinical element, because there will be no grid list of clinical element items displayed during Chart Review for a SUMMARY type clinical element configuration.
Previous
Go to the previous step in the Create Clinical Element Configuration wizard.
Figure 11. Admin – Create Clinical Element Configuration – Step 3 – Preview Output
Table 10: Admin – Create Clinical Element Configuration – Step 3 – Preview Output
Figure 12. Admin – Create Clinical Element Configuration – Step 4 – Name and Description
Table 11: Admin – Create Clinical Element Configuration – Step 4 – Name and Description
Start Over
Clear out all data from the wizard and start over defining the clinical element configuration.
The Projects item in the Admin drop down menu takes you to the pages that allow you to define your projects, their processes, tasks, and database mappings, etc. First, an annotation project specifies a connection to a project database. This database will be used to pull clinical element information, the chart, notes, and records that are relevant to the planned chart review workflow. Next, a project has documents that describe the annotation work that is to be done on the project. These may be included as annotation task instructions that will be sent to an annotator that is assigned a task to perform. In addition, a project is associated with system users. While a project is owned by a particular user, other users can be assigned to a project with designated project roles which give them appropriate permissions on that project. Finally, a project defines the annotation process workflows that need to occur to get the work of annotation done on a project. These processes detail the tasks that need to be performed by the annotators, and which tasks require pre-annotations and how generated annotations will be grouped and used.
Project processes utilize pre-loaded process templates that give structure to the process and can be reused by multiple projects. In addition to a process templates, a library of annotation schemas is maintained at the system level, so that they may be reused in multiple projects.
Figure 13. Admin – Project List
Table 12: Admin – Show Project – General Configuration
Name Column
Sorts the table by project name.
Takes you to the pages that show the specified project.
The name of the project
A short description of the project.
View
Takes you to the pages show the specified project.
Takes you to the pages to edit the specified project.
Deletes the specified project.
Takes you to the previous page of projects.
Takes you to the next page of projects.
Create Project
Creates a project and takes you to the pages to edit that project.
Figure 14. Admin – Project – Show – General Configuration
Table 13: Admin – Project – Show – General Configuration
Project Name
The name of the project.
A brief description of the project.
Database Connection URL
This is the jdbc connection string to the project database (i.e. jdbc:mysql://localhost/chartreview?useUnicode=yes&characterEncoding=UTF-8).
JDBC Driver
The jdbc driver used to connect to the project database (i.e. com.mysql.jdbc.Driver).
JDBC Username
Username to log into the project database.
JDBC Password
Password to log into the project database.
Run SQL Query
Takes you to the page that allows you to run an SQL query against the project database.
Drop Siman Tables
Drops the Siman tables from the project database.
Update Annotation Text
Annotations save a copy of the text that was spanned with than annotation swipe, as well as the start and end offsets of that span. This utility function refreshes the copy of the spanned text in all annotations in the project by querying the original documents with the annotation span anew. This action may be used if annotations are imported that do not save spanned text, for example.
Delete Project
Deletes the entire project!
Siman Tables Exist
Siman tables exist in the project database – no action required.
Siman Tables Do Not Exist
Chart Review requires that Siman tables exist in the project database. Siman tables hold annotation information and are a standard integration framework for sharing annotations with other systems like UIMA NLP Pipelines and CHEX annotation validation.
Create Siman Tables
Creates the Siman tables in the project database.
Figure 15. Admin – Project – Show – Documents
Table 14: Admin – Project – Show – Documents
The name of the documents that are associated with the project. Project documents can be included in an annotation workflow process task to allow an annotator to better understand the annotation task given him.
A brief description of the project document.
Opens a new browser tab to display the selected project document.
Deletes the project document from the project database.
Upload Document
Name of the document to upload to the project.
A brief description of the document that will be displayed during Chart Review to an annotator if this document is included as a task description.
Document
The document to upload.
Browse the local browser file system for a document to upload.
Uploads the document to the project database.
Figure 16. Admin – Project – Show – Project Users
Table 15: Admin – Project – Show – Project Users
Username
The name of a user that has a role in this project.
Role
The role of a user on this project (i.e. ROLE_ADMIN, ROLE_USER).
Figure 17. Admin – Project – Show – Processes
Table 16: Admin – Project – Show – Project Users
Refresh
Refreshes the list of process of this project.
Process
Running/Historic
Copies the specified process and takes you to the pages to edit that process.
Deletes the process!
Takes you to the pages to view the specified process.
Add Process
Adds a process to the project and takes you to the pages to edit that process.
Figure 18. Admin – Project – Edit – General Configuration
Table 17: Admin – Project – Edit – General Configuration
Takes you to the Project Users tab in the project editor.
Figure 19. Admin – Project – Edit - Project Users
Table 18: Admin – Project – Edit – Project Users
Remove
Removes the user from the project.
Find User
Name of the user to find in the system.
Add
Adds username in the text field Find User as a user in the project.
Note: If the user is not a valid system user, an error message will be displayed.
Takes you to the General Configuration tab.
Updates the project with the edited project values.
Figure 20. Admin – Project – Add Process – Step 1 – Choose the Process to Add
Table 19: Admin – Project – Add Process – Step 1 – Choose the Process to Add
Select process
The process template type that the process will be modeled from. For example, a single step process or a multi-step process, etc. Process templates can be uploaded in the Admin -> Process menu.
Takes you to the next step in the process creation wizard.
Figure 21. Admin – Project – Add Process – Step 2 – Process Parameters
Table 20: Admin – Project – Add Process – Step 2 – Process Parameters
Process Name
The name of the process that is presented in Chart Review
Clinical Element Group
This is an optional grouping that will keep all clinical elements grouped under a specified group. Generally this should be left blank. This essentially allows for multiple copies of the same clinical element “document”. Annotations created on one copy of a clinical element could never be seen on another copy of the clinical element, in, for example, a subsequent “downstream” process.
Process Steps
There will be one tab for each step (task) that is defined in the chosen process type workflow.
Schema
The annotation schema that an annotator will use during Chart Review to perform the annotation task required in this step of the annotation process workflow. Schemas are defined through the Admin -> Schema menu item.
Clinical Elements
The clinical elements that will be displayed as context to the principal clinical element displayed in Chart Review. The principal clinical element is the clinical element that the task is focused on, for example a patient is a common principal clinical element. Along with the principal clinical element, an annotator may need to see other contextual clinical information that would support the annotation of the principal clinical element. For example, to classify a patient for a given study, an annotator may need to see clinical notes, lab values, and radiology reports, but he may not need to see medication or problem lists.
Note that in Chart Review, context clinical elements may be annotated as well as the principal.
Include/exclude all clinical elements
A convenience toggle for including/excluding all listed clinical elements.
Include
If checked, the specified clinical element will be available to be displayed in Chart Review when an annotator performs this task.
Hidden
If checked, the specified clinical element will not be displayed automatically when an annotator initially retrieves this task.
Clinical Element
Name of the clinical element.
Position
The order in which the specified clinical element view will appear in Chart Review. For example, a clinical element with position 1 will appear in the top priority visual position in the application browser window layout. Positions do not have to be sequential: included clinical elements with positions of 1, 3, and 5 will be seen in the same order as if they had positions 1, 2, and 3.
Task Name
The name of the task that is presented in Chart Review
Annotation Group
Annotations created for this task will be stored with this annotation group. Annotations may be included in downstream process tasks as pre-annotations by specifying this annotation group as the Task Pre-Annotation Group of the subsequent process task.
Task Pre-Annotation Group
The annotation group to load as pre-annotations to this task. If there are multiple pre-annotation groups, separate them with a SEMI-COLON AND NO SPACES. For example: group1;group2;group3.
Task Principal Clinical Element
Usually this is the patient clinical element. More generally, this is the clinical element for which a task is created. The purpose of the task is to present for annotation this clinical element. All other clinical element information is contextual to performing the task on this clinical element.
Task Documentation
A description of what needs to be done to accomplish this task. The target audience is an annotator. This description is displayed in the Chart Review task panel. If this description is long or needs graphics, consider uploading a document to the project (Admin -> Project -> Documents) and selecting that document in Associated Project Document For This Task below.
Associated Project Document For This Task
A project document that describes what needs to be done to accomplish this task. The target audience is an annotator.
Takes you to the previous page in the Create Process wizard.
Takes you to the next step in the Create Process wizard.
Figure 22. Admin – Project – Add Process – Step 3 – Users and Clinical Elements In This Process
Table 21: Admin – Project – Add Process – Step 3 – Users and Clinical Elements In This Process
Task Creation Query
Query to select a list of principal clinical element ids (i.e. patient ids). A task is created for each clinical element id returned.
Users
Select all users that could perform this task. Users may be added to a project in Admin -> Project.
Other
Assignment Style
When an annotator gets a new assignment in Chart Review, an assignment style of BY PROCESS dedicates all tasks in a process to the annotator. That annotator must complete all tasks in the assigned process. An assignment style of BY TASK dedicates only one task to the annotator. Other tasks in the process may be completed by other annotators, or by this annotator, whoever is available first.
Takes you to the previous page of the Create Process wizard.
Create Tasks and Finish
Saves the process information and creates all tasks for the process. These tasks are saved in a queue waiting for an annotator to get a new assignment in Chart Review.
Figure 23. Admin – Project – Run SQL Query
Table 22: Admin – Project – Run SQL Query
SQL To Run
Any select statement to run against the project database. This is a convenience feature, allowing discovery of project database data that may be needed for project definition, management, or maintenance.
Note: Updates and deletes and DDL with fail.
Execute
Execute the query
The Reports item in the Admin drop down menu takes you to pages that allow perusal of analytical reports about various aspects of any of your projects, including task completion, annotations made, inter-annotator agreement, etc.
Figure 24. Admin – Chose Project and Processes For Reports
Table 23: Admin – Chose Project and Processes For Reports
Project
The project to be reported on.
Processes
The processes of the project to be reported on.
Select
Sets the project and processes for which reports from the report page will be given.
Figure 25. Admin – Reports
Table 24: Admin – Reports
More…
Takes you to a popup displaying the project name and a list of all processes in that project.
Takes you back to the Choose Project and Processes For Reports page to pick another project and processes to report on.
Back to reports
Takes you back to the list of reports available.
How Many Annotations By Type
A report of how many annotations were created for each classification found in the process task schemas.
How Many Annotations By Annotator And Type
A report of how many annotations were created for each classification found in the process task schemas, listed by which annotator created the annotations.
Patients Per Annotator and Process
A report of how many patients were annotated by each annotator for each process.
Patients Per Annotator and Process Detail
A report of which principal clinical elements (i.e. patients) that were annotated by which annotators for the process tasks.
Patients Reviewed by More Than One Annotator
A report of how many times each principal clinical element (i.e. patient) has been reviewed by an annotator.
Inter-Annotator Agreement
A report of inter annotator agreement using a Fleiss’ kappa by principal clinical element (i.e. patient), by classification, by annotator.
Figure 26. Admin – Report – Annotations Per Annotator Detail
Table 25: Admin – Report – Annotations Per Annotator Detail
Export to CSV
Opens the report in Microsoft Excel or saves a CSV to the local file system.
Show N entries
The number of rows to display per page.
Search
Filters the list by the given string (word/partial word).
Note: The string can be found in any of the columns of the table.
The process for which the report was generated.
Annotator
The annotator that created the annotation.
The name of the clinical element configuration type of the clinical element of the annotation. Clicking on this name allows you to view the content of the clinical element that was annotated.
Task
The id of the task the annotation was created for. Clicking on this id takes you into Chart Review to review or change that completed task.
Patient
The principal clinical element (i.e patient) that was annotated.
Annotation Type
The classification from the project task annotation schemas of the annotation.
Covered Text
The clinical element content text that was highlighted by the annotation (if any).
Attributes
A list of the annotation features (name/value pairs).
Showing x to y of N entries
The current location of the page within the data.
Previous…Page Numbers…Next
Move between pages of the report.
Figure 27. Admin – Report – Annotations Per Annotator Detail – Clinical Element
Table 26: Admin – Annotations Per Annotator Detail – Clinical Element
Clinical Element Content
The content of the clinical element.
Figure 28. Admin – Report – How Many Annotations By Type
Table 27: Admin – Report – How Many Annotations By Type
Filters the list by the given string (word/partial word). Note: The string can be found in any of the columns of the table.
The classification type of the annotations counted.
Count
The number of annotations of the given classification type.
Figure 29. Admin – Report – How Many Annotations By Annotator And Type
Table 28: Admin – Report – How Many Annotations By Annotator And Type
The annotator that created the annotations represented in the count by type.
Figure 30. Admin – Report – Patients Per Annotator and Process
Table 29: Admin – Report – Patients Per Annotator and Process
The process from which the patient count by annotator is found.
The annotator that created the annotations represented in the count.
Patient Count
The number of annotations created by the given annotator for the given process.
Figure 31. Admin – Report – Patients Per Annotator And Process DETAIL
Table 30: Admin – Report – Patients Per Annotator and Process DETAIL
The process from which the principal clinical element (i.e. patient) annotation task was performed.
The annotator that performed the principal clinical element (i.e. patient) annotation task.
Task Id
The id of the annotation task from which the principal clinical element (i.e. patient) annotation task was performed.
Patient Id
The id of the principal clinical element (i.e. patient) on which the annotation task was performed.
Figure 32. Admin – Report – Patients Reviewed More Than Once
Table 31: Admin – Report – Patients Reviewed More Than Once
The principal clinical element (i.e. patient) that was reviewed more than once.
Reviewed Count
The count of times that the principal clinical element (i.e. patient) was reviewed.
Figure 33. Admin – Report – Inter-Annotator Agreement – Original Report
Table 32: Admin – Report – Inter-Annotator Agreement – Original Report
k (Fleiss’ kappa)
A statistica measure for assessing the reliability of agreement between a fixed number of annotators when assigning categories to a number of patients. See: en.wikipedia.org/wiki/Fleiss’_kappa
concordence
The average of the Pi column.
Left column values
The principal clinical element ids (i.e. patient).
Top row values
Annotation schema categories of annotations.
Cell
Number of annotators annotating an annotation schema category.
Figure 34. Admin – Report – Inter-Annotator Agreement – New Report
Table 33: Admin – Report – Inter-Annotator Agreement – New Report
Number of annotators annotating an annotation schema category listed by annotator.
The Schemas item in the Admin drop down menu takes you to the pages that allow perusal and definition of a library of annotation schemas that is shared by all users and all projects. These annotation schemas define the classifications, and class attributes that will be used to perform the work of an annotation task.
Chart Review annotation schemas provide the following basic entities:
· Classifications
· Attributes (text, numeric, date, option list) – can be reused on classifications
Figure 35. Admin – Schema List
Table 34: Admin – Schema List
Sorts the schema list by schema name.
Takes you to the pages that edit the specified schema.
The name of the schema.
Takes you to pages to edit the specified schema.
Deletes the specified schema!
Copes the specified schema and takes you to the pages to edit it.
Opens a new tab in the browser and displays the specified schema in XML format. This format can be uploaded in another project or another Chart Review system deployment.
Previous…123…Next
Standard list paging mechanism.
Create Schema
Creates a schema and takes you to the pages to edit it.
Upload New Schema
Uploads a new schema from XML file to the database.
Brows the local browser file system for a schema file to upload.
Submit Query
Uploads the schema file.
Figure 36. Admin – Schema – General Configuration
Table 35: Admin – Schema – General Configuration
A brief description of the schema.
Delete Schema
Deletes the schema!
Done
Saves the changes to the schema and takes you to the Schema List page.
Figure 37. Admin – Schema – Attributes
Table 36: Admin – Schema – Attributes
The name of the class attributes.
The type of class attribute (i.e. Text/Numeric/Date/Options).
Min
The minimum valid numeric or date value.
Max
The maximum valid numeric or date value.
Options
The list of options for an option type class attribute.
Takes you to pages to edit the specified class attribute.
Deletes the specified class attribute!
Copes the specified class attribute and takes you to the pages to edit it.
Create Class Attribute
Creates a new class attribute and takes you to the pages to edit it.
Figure 38. Admin – Schema – Attribute – Create/Edit
Table 37: Admin – Schema – Attribute – Create/Edit
The name of the class attribute.
The type of the class attribute (i.e. Text/Numeric/Date/Option). An option attribute is presents a list of valid options from which to choose during Chart Review).
Delete Attribute
Deletes the attribute!
Saves the changes to the attribute and takes you to the Create/Edit Schema page.
Figure 39. Admin – Schema – Attribute – Create/Edit - Numeric
Table 38: Admin – Schema – Attribute – Create/Edit - Numeric
When numeric type is chosen, Numeric Low and Numeric High fields appear to specify a valid numeric range for the attribute.
Numeric Low
The minimum valid numeric value.
Numeric High
The maximum valid numeric value.
Figure 40. Admin – Schema – Attribute – Create/Edit - Date
Table 39: Admin – Schema – Attribute – Create/Edit - Date
When date type is chosen, Min Date and Max Date fields appear to specify a valid date range for the attribute.
Min Date
The minimum valid date value.
Max Date
The maximum valid date value.
Figure 41. Admin – Schema – Attribute – Create/Edit - Option
Table 40: Admin – Schema – Attribute – Create/Edit - Option
When option type is chosen, an options list and create button appear to allow valid options to be specified.
The list of valid option values for the option attribute.
The name of the option.
Takes you to the pages to edit the specified option.
Deletes the specified option!
Copies the specified option and takes you to the pages to edit it.
Create Option
Creates an option and takes you to the pages to edit it.
Figure 42. Admin – Schema – Attribute – Create/Edit - Option - Create/Edit Option
Table 41: Admin – Schema – Attribute – Create/Edit - Option
Delete Option
Deletes the option!
Saves the changes to the option and takes you to the Create/Edit Attribute page.
Figure 43. Admin – Schema – Classifications
Table 42: Admin – Schema – Classifications
The name of the classification.
Color
The color of the classification. This is the highlight color of an annotation span with this classification.
The list of attributes of this classification.
Create Classification
Creates a classification and takes you to the pages to edit it.
Figure 44. Admin – Schema – Classification – Create/Edit – General Configuration
Table 43: Admin – Schema – Classification – Create/Edit – General Configuration
Color Label
Shows how the color will look in a highlight.
Delete Classification
Deletes the classification!
Saves the changes to the classification and takes you to the Create/Edit Schema page.
Figure 45. Admin – Schema – Classification – Create/Edit – Attributes
Table 44: Admin – Schema – Classification – Create/Edit - Attributes
The color of the attributes. This is the highlight color of an annotation span with this classification.
Available Attributes
A list of reusable attributes defined at the schema level that can be added as class attributes.
Add Attributes
Add the selected attributes to the classification as class attributes.
Creates a new available class attribute and takes you to the pages to edit it. The resulting attribute shows up in the list of Available Attributes, but still needs to be added to the classification.
Saves the changes to the classification and takes you to the Schema Create/Edit page.
The Failed Jobs item in the Admin drop down menu takes you to a list of failed workflow processes.
Figure 46. Admin – Failed Jobs
The Process Templates item in the Admin drop down menu takes you to the pages that allow upload and definition of process pre-defined process templates that may be used in creating process instances for a given project. Any xml file containing a process definition that uses the BMP 2.0 standard can be loaded. For example, a process defined using Activi Designer will can be loaded. Simple single step and multi-step processes should work in Chart Review. More complex process configurations have not yet been tested.
Figure 47. Admin – Process Templates
Table 45: Admin – Process Templates
Process List
List of process templates available to use when creating a process for a project. This template describes the different tasks that need to be defined and executed as part of an annotation process workflow. It follows the BMP 2.0 process definition standard.
ID
The id of the process template.
Name of the process template presented in the Project process definition.
Description of the process template.
Version
Version of the process template.
Diagram
Diagram of the process template. Clicking on the diagram button opens a new browser window and displays the diagram.
Deletes the process template!
Upload Process Template
Allows upload of any xml file containing a process definition that uses the BMP 2.0. For example, a process defined using Activi Designer will can be loaded. Simple single step and multi-step processes should work in Chart Review. More complex process configurations have not yet been tested.
Find the BMP 2.0 xml process definition file in the browser’s local file system.
Uploads the process template to the database.
The Process Templates item in the Admin drop down menu takes you to the pages that provide tools and utilities to kill processes and view API documentation, for example.
Figure 48. Admin - Tools and Utilities
Table 46: Admin – Tools and Utilities
Admin Tools
Area for various system administration activies.
Delete all running Actviti Process Instances – Do Delete
Deletes all processes and tasks from all projects!!! Annotations from any of those tasks will not be deleted, but an annotation’s association with the task for which it was generated will no longer exist.
Rest API
Area to access various API documents.
View Rest API Docs
Takes you to pages to view the Chart Review API documents generated by the JSONDoc subsystem. To get back from these pages, press the browser back button, because the Chart Review banner will not be available in this page space.
Figure 49. Admin - Tools and Utilities – API Docs
Table 47: Admin – Tools and Utilities – API Docs
Various
These pages describe the web services the available in Chart Review to get and submit annotations, clinical element configurations, and annotation schemas programmatically. To get back from these pages, press the browser back button, because the Chart Review banner will not be available in this page space. A detailed description of how to use these pages is out of the scope of this document. Please see JSONDoc documentation for details.
The Process Templates item in the Admin drop down menu takes you to the pages that allow user definition and maintenance.
Figure 50. Admin - Users
Table 48: Admin – Users
Username Column
Sorts the user list by username.
The name of each user.
Username link
Takes you to the pages to show user information.
Account Non Expired Column
Sorts the user list by account non-expired status.
Account Non Expired
True if the user account is active. False if the user account exists but is expired. The user cannot use the account. See the system administrator to reset.
Account Non Locked Column
Sorts the user list by account non-locked status.
Account Non Locked
True if the user account is NOT locked. False if the user account exists, but is currently locked. This is usually automatically set because of invalid login attempts. The user may not used the account. See the system administrator to reset.
Credentials Non Expired Column
Sorts the user list by credentials non-expired status.
Credentials Non Expired
True if the current password is not expired. This is set this to False to force the user to enter a new password.
Enabled Column
Sorts the user list by enabled status.
Enabled
True if the user account is enabled. False if the user account has been disabled by the system administrator. See the system administrator to find out why.
Figure 51. Admin – Show User
Table 49: Admin – Show User
User List link
Takes you back to the User List.
Authorities
A list of the roles that the user has on various projects.
Takes you to the pages to edit the user account definition.
Deletes the user!
Figure 52. Admin – Edit User
Table 50: Admin – Show User
Saves the changes to the User account.
The About item in the Admin drop down menu takes you to the pages that show information about the application, its version, structure, dependencies, and components.
Figure 53. Admin - About
Table 51: Admin – About
Application Status
Version information about Chart Review and its major technology subsystems. Counts of system components.
Installed Plugins
A list of the plugin components used by this application with their version numbers.
Available Controllers
These links call the various controllers they represent. These may be used for system understanding and programmer testing.
Figure 54. Admin - About – API Docs
Table 52: Admin – About – API Docs
The Log Level item in the Admin drop down menu takes you to the pages that allow control over the various levels of system logging available.
Figure 55. Admin - Log Level
Table 53: Admin – Log Level
Controller Loggers
Allows you to set the logging level that Grails controllers use to log to the chart-review log file found in the Tomcat logs directory.
Service Loggers
Allows you to set the logging level that Grails services use to log to the chart-review log file found in the Tomcat logs directory.
Domain Class Loggers
Allows you to set the logging level that Grails domain classes use to log to the chart-review log file found in the Tomcat logs directory.
Grails Loggers
Allows you to set the logging level that Grails itself uses to log to the chart-review log file found in the Tomcat logs directory.
3rd Party Loggers
Allows you to set the logging level that Grails 3rd party plugins use to log to the chart-review log file found in the Tomcat logs directory.
The Performance Monitoring item in the Admin drop down menu takes you to the pages that show performance monitoring analytics about the Chart Review system itself.
Figure 56. Admin – Performance Monitoring – Top
Figure 57. Admin – Performance Monitoring - Bottom
Table 54: Admin – Performance Monitoring
These pages describe the performance of the Chart Review system as tracked by the JavaMelody monitoring subsystem. To get back from these pages, press the browser back button, because the Chart Review banner will not be available in this page space. A detailed description of how to use these pages is out of the scope of this document. Please see JavaMelody documentation for details.
Chart Review is a web application that allows manual annotations to be made on multiple elements and multiple levels of a medical chart simultaneously. The task of classifying a cohort of patients can be done as a patient is reviewed in the full context of his clinical notes, labs, procedures, problems and medications. Or a corpus of notes can be annotated in the context of the patient, labs, problems, procedures and medications that clarify the notes. The type and set of clinical elements that can be viewed as part of an annotation task is completely customizable and configurable by an annotation project administrator.
Figure 58. Chart Review
Annotators who have been assigned to an annotation project can open Chart Review with a new or previous assignment that they have been given from the an annotation process defined in the project and see the requirements of the task and all of the information necessary to perform the annotation task that has been assigned. Annotators can finish a task, move to another task, or put a task on hold. Within the Chart Review tool, an annotator can peruse a chart independent of the annotation task at hand (he can collapse the annotation panel entirely), or he can be taken to the parts of the chart that have been pre-annotated by sorting, filtering, grouping, and selecting annotations from the annotation list that show features of interest in the chart. In addition, the annotator has control over the content and layout of the chart presentation as well as the annotation list. The following sections describe how the Chart Review tool can be used to accomplish an annotation task.
The following outlines the basic annotation workflow steps, starting from the Chart Review Home page:
1. Pick a project and process
2. Press Get Next Assignment
3. Find out what annotation is required by pressing the Task Info button in the task panel
4. Select the appropriate schema classification for the task
5. Scroll to the clinical element view
6. Select a clinical element item
7. Scroll to the desired place in the content text
8. Highlight the desired text (an annotation will appear in the annotations list on the left)
9. Fill out any annotation attribute features presented in the annotation editor panel on the lower left
10. When annotation is finished, press Submit/Next to submit the annotations and get the next task
That’s it!
A user can see his recent task work for a given project and process, including work on completed processes. A user can fetch a new task assignment or work on existing open assignments, or assignments that have been put on hold.
Figure 59. Chart Review – Initiating a Chart Review
Table 55: Chart Review – Initiating a Chart Review
The project you want to perform an annotation task on.
Show Completed Processes
If checked, completed processes are provided in the Process dropdown as well as incomplete processes.
The project process workflow you want to perform an annotation task on.
Get Next Assignment
Gets a new task assignment from the chosen project process and initiates chart review on that task. The task moves to an ASSIGNED state.
Note that the processes listed in the Process dropdown show how many unassigned tasks they have left.
Your Recent Work
This is a list of tasks that have been assigned to you for the specified project process. These tasks may be open, on hold, or completed.
Task Id link
Initiates chart review on the specified task.
The id of the task.
ASSIGNED/COMPLETED
Status
open/hold/completed
Comment
A comment that was added for a hold.
The date/time the task was assigned or completed.
A reviewer has several layout options available, including:
Two column mode allows a user to have two instances of the same type of clinical element view open side by side for comparison. For example, a user could open a note that was annotated well, according to the task standard and use it to guide annotation of another note of the same type of clinical element.
Figure 60. Chart Review – Two Column Mode
Figure 61. Chart Review – Single Column Mode
Table 56: Chart Review – Two Column Mode
Two Column Mode Toggle (app upper right)
Toggles between two columns and one column, distributing the views between the two columns or coalescing them into one column.
Auto-Select
View height can be adjusted by dragging the bottom or top borders of the view window.
Figure 62. Chart Review – Variable Height Views
Table 57: Chart Review – Variable Height Views
Drag View Top/Bottom
Adjusts the height of the view.
A clinical element view of type LIST has a grid part and a detail part. The user may change the docking of the detail panel to the right or the bottom. He may also choose to hide the detail panel altogether through the Detail dropdown button
Figure 63. Chart Review – View Detail Docking/Hiding Options
Table 58: Chart Review – Variable Height Views
Detail Right (default)
Shows the detail at the right of the view.
Detail Bottom
Shows the detail at the bottom of the view.
Detail Hide
Hides the detail from the view.
Columns may be optionally included/excluded from the grid view. Column inclusion/exclusion is toggled through the column header dropdown menu.
Figure 64. Chart Review – Optional Column Inclusion
Table 59: Chart Review – Optional Column Inclusion
Dropdown on Right of Colum -> Columns
Toggles the visibility of each column that has Include checked in the process task definition.
The grid list may be sorted ascending/descending by any of the columns. Column sorting is toggled through the column header dropdown menu.
Figure 65. Chart Review – List Sorting
Table 60: Chart Review – List Sorting
Dropdown on Right of Column -> Sort Ascending/Descending
Sorts by the column values ascending or descending. An indicator is displayed on the column header to show column sort and direction.
The grid list may be grouped by any of the columns. Column grouping is toggled through the column header dropdown menu.
Figure 66. Chart Review – List Grouping
Table 61: Chart Review – List Grouping
Dropdown on Right of Colum -> Group by this Field
Groups the grid list by the specified column.
Note: The list can be both grouped and sorted simultaneously.
Dropdown on Right of Column -> Show in groups
Toggles the grouping by the specified column.
Figure 67. Chart Review – Variable Column Order and Size
Table 62: Chart Review – Variable Column Order and Size
Drag Column Order/Size
Columns can be reordered by dragging and they can be resized by grabbing the edge of the column headers. These changes persist until the view is closed. Two views of the same type may have different column layouts.
Figure 68. Chart Review – Collapsible Views
Table 63: Chart Review – Collapsible Views
Collapse/Expand View
Collapses or expands a view.
Figure 69. Chart Review – Delete View
Table 64: Chart Review – Delete Views
Delete View
Deletes the view. Another instance of a view type can be added through the Add View dropdown menu.
Figure 70. Chart Review – Add View
Table 65: Chart Review – Add View
Add View
Adds an instance of the specified view type. Multiple instances of the same view type are allowed.
Two instances of the same type of view can be opened simultaneously, affording a comparison capability where the annotation on one document of a given type may be used as a model for annotating another document of a given type, for example.
Note that when an annotation is created on one type of clinical element, all views of that type of clinical element will be auto-selected to show the annotation, unless the Auto-select toggle is OFF. Turn the Auto-select toggle off when comparing two documents of the same clinical element type so that the reference document will not be changed as annotations are added to the second document of that type.
Figure 71. Chart Review – Multiple Instances of the Same View (Comparison)
Figure 72. Chart Review – Auto-select Toggle
The annotation panel can be collapse if the user wants more room for chart review activities.
Figure 73. Chart Review – Closable Annotation Panel
Table 66: Chart Review – Closable Annotation Panel
Collapse Annotation Panel
Collapses/expands the annotation panel.
There are several features of the Chart Review interface that support project workflow issues, including saving a detail view as a separate tab to refer to later, and a Done button to keep track of items for which the task has been completed.
A user can save a detail view as a separate tab so that he may come back to it at a later point.
Note: The column that is displayed as the tab title is specified in the Title Field of the clinical element definition.
Figure 74. Chart Review – View in New Tab
Table 67: Chart Review – View In New Tab
View in new tab
Opens the current detail in a separate tab. Annotations selected in the annotation list will be auto-selected and viewed in a separate tab, if there is a separate tab opened for that clinical element. If there is not a separate tab for that clinical element, the auto-select view will show it in the detail panel as usual.
To help a user keep track of which clinical elements he has already performed the annotation task on, he may mark the element as Done. Clinical elements that are done have a check mark by them in the grid.
Note that the task may be marked as done by pressing the Done button in the Task panel. The task is marked as completed and the user is returned to the Chart Review home page.
Figure 75. Chart Review – Marking Records As Done
Table 68: Chart Review – Marking records as Done
Toggles the clinical element between done and not done. Done is indicated by a green checkmark in the grid.
The user may allow cell text in a clinical element view grid to be wrapped or truncated.
Figure 76. Chart Review – Optional Text Wrapping
Table 69: Chart Review – Optional Text Wrapping
Wrap
Toggles wrapping of text in the grid cells. If wrapping is off, the text in a cell is truncated. If wrapping is on, cell text is wrapped and the row height is increased.
Each row of a clinical element view grid may display a description or not by toggling with the Description toggle button.
Note: The column that is displayed as the description is specified in the Description Field of the clinical element definition.
Figure 77. Chart Review – Description Hiding
Table 70: Chart Review – Description Hiding
Toggles display of the clinical element description in the grid as a preview.
All interaction with the task that is being performed in Chart Review is displayed in the Task panel in the upper left part of the application screen, at the top of the Annotation panel. The name of the task is displayed, along with the task id in parenthesis. The task id may help in referencing the task in reports and when choosing the task again from the Chart Review Home page’s Your Recent Work list. A user may also view a brief description of the task, or a detailed description of the task to understand the nature of the work he has been assigned. Finally, the user may choose how to change the task status after the task is done being performed.
Figure 78. Chart Review – Task Panel and Toolbar
Table 71: Chart Review – Task Panel and Toolbar
Task Name and Task Id
The name of the task and the task id (in parenthesis).
Note The task id may help in referencing the task in reports and when choosing the task again from the Chart Review Home page’s Your Recent Work list.
Principal
The type of the principal clinical element upon which the task is being performed.
Documentation
A somewhat brief description of the task to be performed.
Note: The Task panel is scrollable, allowing the user to view a longer description.
Prompts for save, if needed, and exits Chart Review.
Save
Save annotations, but keeps the current task open.
Hold/Next
Save annotations and submit the task as being on-hold until later. Get the next task assignment.
Submit/Next
Save annotations and submit the task as completed. Get the next task assignment.
Task Info
View the detailed task information. A poup-up window is displayed with task information in it. Press close to close the task information window.
Note: If a pdf document, for example, is included in the process task definition as documentation for the task, a separate tab will be opened in the browser to display that document.
The annotation schema associated with the given task is displayed in a collapsible tree in the Annotations schema panel. All classifications available in that schema are displayed and may be selected. To annotate a clinical element text, first select the desired classification and then highlight the text. To annotate a whole clinical element, first select the desired classification and then press the Classify button on the selected clinical element.
Figure 79. Chart Review – Annotation Schema
Table 72: Chart Review – Annotation Schema
Select Classification
The currently selected classification will be used in creating annotations on clinical element text and on whole clinical elements.
Note: If you try to highlight before picking a classification from the annotation schema, an error message is displayed.
Clinical element text may be annotated by selecting an annotation schema classification in the Schema panel and then highlighting the text with a swipe. Annotation spans may overlap in all combinations of ways. Annotation span colors are blended to show overlaps. An annotation appears in the annotation list for every highlight swipe made in the text. Features for that annotation are displayed and able to be edited in the Annotation Editor panel at the lower left of the screen.
Figure 80. Chart Review – Annotation of Clinical Element Text
Table 73: Chart Review – Annotation of Clinical Element Text
Highlight
Creates an annotation which is displayed in the list on the left.
Note: When you create an annotation by highlighting the text, an annotation will be created in the annotation list and annotation features that need to be filled in will be displayed in the Annotation Editor panel at the bottom left of the screen.
Select Annotation from Text
When you click on an annotation span in the text, the corresponding annotation item will be selected in the Annotation List to the left.
Note: A selected annotation is show with black under and over lining in the text.
Select Annotation from List
When you select an annotation in the Annotation List on the left, the clinical element to which the annotation belongs will be opened and the annotation will be scrolled into view and shown as selected.
A whole clinical element may be annotated by selecting a classification in the Schema panel and pressing the Classify button found in the detail area of the clinical element view. A clinical element may have multiple classifications. Each classification is displayed to the right of the Classify button.
Figure 81. Chart Review – Annotation of Whole Clinical Element
Table 74: Chart Review – Annotation of Clinical Element Text
Classify
Creates an annotation for the whole clinical element record which is displayed in the list on the left.
Note: When you create an annotation by pressing the Classify button, an annotation will be created in the annotation list and annotation features that need to be filled in will be displayed in the Annotation Editor panel at the bottom left of the screen.
Select Annotation from Classify panel
When you click on an annotation classification label in the are next to the Classify button, the corresponding annotation item will be selected in the Annotation List to the left.
When you select an annotation for a whole clinical element in the Annotation List on the left, the clinical element to which the annotation belongs will be opened and the annotation will be shown as selected.
The principal clinical element of a task may be displayed (or not) in a view just like the context clinical elements. It is commonly displayed with a Summary tab rather than with the default grid/detail display because the principal clinical element is only one element (i.e. patient), not a list of elements like may of the context clinical elements. It is annotated in the same way as any other clinical element displayed.
Figure 82. Chart Review – Annotation of Principal Clinical Element
All annotations associated with a given task whether they be on the principal clinical element itself or any of the context clinical elements, are displayed in a grid in the Annotation panel. This grid may be grouped, sorted, filtered, and deleted. Selecting annotations in this list will open the corresponding clinical element view (if not already open) and will auto-scroll to the selected annotation. As annotations are created they appear in the list and their features are displayed in the Annotation Editor panel below the list. The grid may be sorted, grouped and filtered by accessing a dropdown menu on the right of the column header.
Figure 83. Chart Review – Annotation List
Table 75: Chart Review – Annotation List
All Annotations / Selected Document Annotations
Toggles between showing all annotations belonging to the task (and all of its clinical element documents) and showing only those annotations belonging to the currently selected clinical element document in the views to the right.
Show Column Filters
Shows the current column filters in a popup message.
Clear Column Filters
Clears all column filters.
Delete Selected Annotations
Deletes all currently selected annotations.
Unless one of the save buttons is pressed, an unintended delete will not be saved to the database. So an unintended delete may be undone by exiting going back to the Chart Review Home page without saving – but, this will not save any other changes as well.
Refreshes the annotation grid.
The annotation grid may be refreshed to display edits that have been made in the Annotation Editor.
Annotations have attributes features that may be edited when an annotation is created or modified at a later time. The attributes are displayed in the Annotation Editor panel immediately when an annotation is created or selected. After editing the attributes, you may need to refresh the Annotation list.
Figure 84. Chart Review – Editing Annotation Attributes
Table 76: Chart Review – Editing Annotation Attributes
Text
Text attributes may be edited by entering text in a simple text field.
Numeric
Numeric attributes may be edited by entering a valid number in a simple text field. If the number is out of range, an indication of the invalid state of the field will be indicated with a red border and a popup stating what is invalid.
Date attributes may be edited by entering a valid date in a simple text field or by picking a date from a date picker. If the date is out of range, an indication of the invalid state of the field will be indicated with a red border and a popup stating what is invalid.
Option
Option attributes may be edited by choosing an option from the dropdown menu.
Index
3
3rd Party Loggers, 72
A
About, 69
About – API Docs, 70
Account Non Expired, 65, 66, 68
Account Non Expired Column, 65
Account Non Locked, 66, 67, 68
Account Non Locked Column, 65
Active, 9, 10
Active link, 9
Add, 29
Add Attributes, 60
Add Process, 27
Add Process – Step 1 – Choose the Process to Add, 30
Add Process – Step 2 – Process Parameters, 31
Add Process – Step 3 – Users and Clinical Elements In This Process, 34
Add View, 89
Admin Tools, 63
All Annotations, 104
All Annotations / Selected Document Annotations, 104
All Elements by Patient Id Query, 17
All Elements By Patient Id Query, 11, 13
Annotation, 101, 103
Annotation Attributes, 105, 106
Annotation Group, 33
Annotation List, 103, 104
Annotation of Clinical Element Text, 99
Annotation of Principal Clinical Element, 102
Annotation of Whole Clinical Element, 101
Annotation of Whole Context Clinical Element, 101
Annotation Panel, 91
Annotation Schema, 98, 99
Annotation Type, 39
Annotation Workflow, 97
Annotations Per Annotator Detail, 38
Annotations Per Annotator Detail – Clinical Element, 40
API Docs, 64, 70
Application Status, 69
Architecture, 1
Assignment Style, 35
Associated Project Document For This Task, 34
Assumptions, xiii
Attribute – Create/Edit, 53
Attribute – Create/Edit - Date, 55
Attribute – Create/Edit - Numeric, 54
Attribute – Create/Edit - Option, 56
Attribute – Create/Edit - Option - Create/Edit Option, 57
Attributes, 52, 60
Authorities, 67
Auto-Select, 80
Auto-select Toggle, 91
Available Attributes, 60
Available Controllers, 70
B
Back to reports, 37, 39, 40, 41, 42, 43, 45, 46, 47, 48
Browse, 10, 11, 50, 63
C
Change, 37, 40, 41, 42, 43, 46, 48
Chart Review, i, 75
ChartReview, 4
Choose the Process to Add, 30
Chose Project and Processes For Reports, 36
Classification, 99
Classification – Create/Edit – Attributes, 60
Classification – Create/Edit – General Configuration, 59
Classifications, 58
Classify, 101
Classify panel, 102
Clear Column Filters, 104
Clinical Element, 33, 39
Clinical Element Configurations, 4
Clinical Element Content, 40
Clinical Element Group, 32
Clinical Element Text, 99, 100
Clinical Elements, 32
Closable Annotation Panel, 91, 92
Collapse Annotation Panel, 92
Collapse/Expand View, 87
Collapsible Views, 87
Color, 59
Color Label, 59
Colum, 83
Column, 84
Column Filters, 104
Column Name, 14, 18
Column Order and Size, 86
Column Order/Size, 86
comparison, 90
concordence, 47, 49
Connection String, 16
Content Template, 15, 20, 21
Content Template Toggle, 19
Context Clinical Element, 101
Controller Loggers, 71
Controllers, 70
Conventions
Documentation, xiii
Copy, 27
Copy To Project, 10
Covered Text, 39
Create Class Attribute, 52, 61
Create Classification, 58
Create Clinical Element Configuration – Step 1 –Define Test Connection and Queries, 16
Create Clinical Element Configuration – Step 2 – Data Set Column Definition & Other Metadata, 18
Create Clinical Element Configuration – Step 3 – Preview Output, 20
Create Clinical Element Configuration – Step 4 – Name and Description, 21
Create Option, 57
Create Schema, 50
Create Siman Tables, 24
Create Tasks and Finish, 35
Create/Edit, 53
Create/Edit – Attributes, 60
Create/Edit - Date, 55
Create/Edit – General Configuration, 59
Create/Edit - Numeric, 54
Create/Edit - Option, 56
Create/Edit - Option - Create/Edit Option, 57
Created By, 11, 13
Created Date, 11, 12, 13
Credentials Non Expired, 66, 67, 68
Credentials Non Expired Column, 66
D
Data Set Column Definition & Other Metadata, 18
Database Connection, 28
Database Connection URL, 23
Date, 55
Define Test Connection and Queries, 16
Delete all running Actviti Process Instances – Do Delete, 63
Delete Attribute, 53, 54, 55, 56
Delete Classification, 59, 61
Delete Option, 57
Delete Project, 24
Delete Schema, 51, 53, 58, 59
Delete Selected Annotations, 104
Delete View, 88
Description, 25
Description Field, 11, 13, 19
Description Hiding, 96, 97
Description link, 9
Detail Bottom, 82
Detail Hide, 82
Detail Right, 82
Disclaimers, xii
Display Name, 14, 18
Do Delete, 63
Conventions, xiii
Symbols, xiii
Documentation Conventions, xiii
Documents, 25
Domain Class Loggers, 71
Done, 51, 53, 54, 55, 56, 57, 59, 94
Drag Column Order/Size, 86
Drag View Top/Bottom, 81
Drop Siman Tables, 24
Dropdown on Right of Colum, 83, 84
E
Edit, 67
Edit – General Configuration, 28
Edit - Project Users, 29
Edit User, 67
Editing Annotation Attributes, 105
Enabled, 68
Enabled Column, 66
Example Patient Id, 17
Exclude, 14
Export, 10
Export to CSV, 39, 41, 42, 43, 45, 46
F
Failed Jobs, 5, 61
Figures, v
Find User, 29
Fleiss’ kappa, 47, 48
G
General Configuration, 10, 23, 28, 51, 59
General Configuration – Edit, 12
General Setup, 6
Get Next Assignment, 77
Grails Loggers, 72
Group, 84, 85
Grouping, 84
H
Hold/Next, 98
Home Page, 3, 4
How Many Annotations By Annotator And Type, 37, 42
How Many Annotations By Type, 37, 41
How to
Use this Manual, xii
How to Use this Manual, xii
I
ID, 62, 63
Include/exclude all clinical elements, 32, 33
Initiating a Chart Review, 76, 77
Inquire
Inquire to File Entries Option, 61, 62, 65
Installed Plugins, 69
Integration, 2
Intended Audience, xii
Inter-Annotator Agreement, 38
Inter-Annotator Agreement – Original Report, 47
J
Jdbc Driver, 16
JDBC Driver, 24, 28
JDBC Password, 24, 28
JDBC Username, 24, 28
Jdbc Username/Password, 17
K
k, 47, 48
Key Field, 14, 19
L
Layout Options, 78
Left column values, 47, 49
Legal Requirements, xii
List Grouping, 84
List item name, 9
List Sorting, 84
Log, 71
Log Level, 5, 71
Loggers, 71
Logout, 6
M
Main Toolbar, 4
Marking Records As Done, 94
Max Date, 55
Min Date, 55
More…, 37, 38, 40, 41, 42, 43, 45, 46, 47, 48
Multiple Instances of the Same View, 90
Multiple Instances of the Same View (Comparison), 90
N
Name, 9, 25, 26, 51, 53
Name and Description, 21
Name Column, 50
Name link, 9, 50
New Clinical Element Configuration, 8
New Report, 48
Next, 17, 30
Numeric, 54
Numeric High, 54
Numeric Low, 54
O
Online Demo, xiii, 1
Option, 56, 57
Option - Create/Edit Option, 57
Optional Column Inclusion, 82, 83
Optional Text Wrapping, 94
Inquire to File Entries, 61, 62, 65
Orientation, xi, xii
Original Report, 47
P
Patient Count, 44
Patient Id, 45, 46
Patients Per Annotator and Process, 37, 43
Patients Per Annotator and Process Detail, 37
Patients Per Annotator And Process DETAIL, 44
Patients Reviewed by More Than One Annotator, 38
Patients Reviewed More Than Once, 46
Performance Monitoring, 5, 6, 72
Plugins, 69
Position, 33
Preview Output, 20
Previous, 35
Previous…123…Next, 50
Previous…Page Numbers…Next, 39, 42, 43, 44, 45, 47
Principal Clinical Element, 102
Process, 77
Process List, 62
Process Name, 32
Process Parameters, 31
Process Steps, 32
Process Templates, 62
Processes, 5
Project – Add Process – Step 1 – Choose the Process to Add, 30
Project – Add Process – Step 2 – Process Parameters, 31
Project – Add Process – Step 3 – Users and Clinical Elements In This Process, 34
Project – Edit – General Configuration, 28
Project – Edit - Project Users, 29
Project – Run SQL Query, 35
Project - Show – Documents, 25
Project – Show – General Configuration, 23, 27
Project - Show – Processes, 27
Project - Show – Project Users, 26
Project Clinical Element Configurations, 8, 9
Project List, 22
Project Name, 23, 28
Project Users, 26, 29
Projects, 5
Q
Quick-Start, 76
R
References, xiii
Refresh, 105
Report – Annotations Per Annotator Detail, 38
Report – Annotations Per Annotator Detail – Clinical Element, 40
Report – How Many Annotations By Annotator And Type, 42
Report – How Many Annotations By Type, 41
Report – Inter-Annotator Agreement – New Report, 48
Report – Inter-Annotator Agreement – Original Report, 47
Report – Patients Per Annotator and Process, 43
Report – Patients Per Annotator And Process DETAIL, 44
Report – Patients Reviewed More Than Once, 46
Reports, 36, 37
Requirements
Legal, xii
Rest API Docs, 70
Reviewed Count, 46
Run SQL Query, 24, 35
Running/Historic, 27
S
Same View, 90
Schema, 99
Schema – Attribute – Create/Edit, 53
Schema – Attribute – Create/Edit - Date, 55
Schema – Attribute – Create/Edit - Numeric, 54
Schema – Attribute – Create/Edit - Option, 56
Schema – Attribute – Create/Edit - Option - Create/Edit Option, 57
Schema – Attributes, 52
Schema – Classification – Create/Edit – Attributes, 60
Schema – Classification – Create/Edit – General Configuration, 59
Schema – Classifications, 58
Schema – General Configuration, 51
Schema List, 49
Schemas, 49
Search, 39, 41, 42, 43, 44, 45, 46
Select Annotation from Classify panel, 102
Select Annotation from List, 100, 102
Select Annotation from Text, 100
Select Classification, 99
Select process, 30
Selected Document Annotations, 104
Service Loggers, 71
Setting up your Browser for Chart Review, 6
Show – Documents, 25
Show – General Configuration, 23
Show – Processes, 27
Show – Project Users, 26
Show Clinical Element Configuration – Columns, 14
Show Clinical Element Configuration – Content Template, 15
Show Clinical Element Configuration – General Configuration, 10
Show Clinical Element Configuration – General Configuration – Edit, 12
Show Column Filters, 104
Show Completed Processes, 77
Show N entries, 39, 41, 42, 44, 45, 46
Show User, 66
Showing x to y of N entries, 39, 41, 43, 44, 45, 47
Siman Tables Do Not Exist, 24
Siman Tables Exist, 24
Single Column Mode, 79
Single Element Query, 11, 13, 17
Single Sign On (SSO) Setup, 6
Sort, 84
Sorting, 84
Start Over, 21, 22
Submit Query, 50
Submit/Next, 98
Switch User, 6, 7
Symbols
Found in the Documentation, xiii
T
Table of Contents, iii
Tables, viii
Task, 39
Task Creation Query, 34, 35
Task Documentation, 33
Task Id, 45, 78
Task Id link, 78
Task Info, 98
Task Name, 33
Task Name and Task Id, 97, 98
Task Panel, 97
Task Panel and Toolbar, 97
Task Pre-Annotation Group, 33
Task Principal Clinical Element, 33
Text, 107
Text Wrapping, 94, 95
Title Field, 11, 13, 19
Toolbar, 4, 97
Tools and Utilities, 5, 63
Tools and Utilities – API Docs, 64
Top row values, 48, 49
Two Column Mode, 78, 79
Two Column Mode Toggle, 80
Two instances, 90
Type Name, 14, 18
U
Update, 14
Update Annotation Text, 24
Upload Document, 25
Upload New Clinical Element Configuration, 10
Upload New Schema, 50
Upload Process Template, 63
User List link, 66, 68
Username, 29, 65
Username Column, 65
Username link, 65
Users, 5, 65
Users and Clinical Elements In This Process, 34
V
Variable Column Order and Size, 86
Variable Height Views, 80, 81
View Detail Docking/Hiding Options, 81, 82
View in New Tab, 93
View In New Tab, 92
View Rest API Docs, 64, 70
W
What is Chart Review?, xi
Whole Context Clinical Element, 101
Workflow, 97
Workflow Support, 92
Wrapping, 95
Y
Your Recent Work, 78
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