Message-ID: <89882062.8662.1711719435485.JavaMail.confluence@ip-172-30-4-17.ec2.internal> Subject: Exported From Confluence MIME-Version: 1.0 Content-Type: multipart/related; boundary="----=_Part_8661_870181889.1711719435482" ------=_Part_8661_870181889.1711719435482 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Content-Location: file:///C:/exported.html 1.4.00 Release Notes

1.4.00 Release Notes

Rele= ase Notes for i2b2 Version 1.4

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These release notes address issues found and information about the i2b2 = version 1.4. Unless otherwise specified, these notes apply to the following= operating systems:

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Additional Informati= on

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Included in this document are the following sections:

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Section

Includes

Installation

Information related to installing the releas= e.

Third Party Software

Software that is utilized by i2b2 but is own= ed, maintained and licensed by other companies is referred to as "Third Par= ty Software". Any version changes made or needed to be made to the users sy= stem will be noted in this section.

New Features

A list of new enhancements will be included = in this section. A brief description and a reference to the specification w= ill be provided.

Updates

Any changes that are not considered an enhan= cement will be included in this section. This may be a fix for a problem fo= und or it may be a change to existing code but not related to a problem.

Licensing

i2b2 licensing information

Trademarks

Trademark information

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Installation

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This release note applies to you if you are upgrading to 1.4 from a comp= uter running an earlier version of the i2b2 workbench. This release contain= s server changes so it is important to update both the client and the serve= r.

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If you are installing 1.4 from a computer running the i2b2 workbench, en= sure that the workbench and all eclipse applications are closed prior to in= stalling this release.

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WHERE DO I START?<= /span>

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Prior to setting up the i2b2 server, workbench or VM Image it is highly = recommended that you read one of the following documents located in the doc= umentation folder.

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1. Hive_Installation_Guide_1-4.pdf

Use for new installations

2. Hive_Upgrade_Guide_1-4.pdf

Use for upgrading existing environment = to 1.4

3. i2b2Workbench_Install_Guide_1-4.pdf

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Use for installing the i2b2 Workbench (= Client)

4. vmware_Install_Guide_1-4.pdf

Use for installing the VM Image

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All of these documents will explain wh= at needs to be done during the setup and in what order.

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<= strong>IMPORTANT INFORMATION REGARDING CHANGE TO PM

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Although the PM Cell itself has not changed, the PM services have been m= odified and a new client has been developed. Gridsphere is no longer the cl= ient used to setup hives, projects and users. The new client resides within= the i2b2 web client and can be found under the heading of "Admin". Further= information regarding the changes can be found in one of the following doc= uments.

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  1. PM messaging document
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  3. PM install document
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<= strong>IMPORTANT CHANGES TO i2b2 VMWARE IMAGE INSTALLATION<= /p>=20

The VMware image of the i2b2 server no longer uses Gridsphere or Tomcat.= The IP address will be displayed on the console once the i2b2 server is st= arted.

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Third Party Software=20

No changes to third party software are required for release 1.4.

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New Features

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i2b2 release 1.4 contains new features that have been outlined below.

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Plu= g-ins Packaged as "Features"

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The i2b2 plug-ins will now be grouped together into an Eclipse feature. = The plug-ins that comprises the i2b2 Workbench will be packaged together as= the i2b2 core features. The core features include the following views in t= he i2b2 workbench.

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  • Analysis
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  • Find Terms
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  • Help
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  • Navigate Terms
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  • Previous Query
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  • Query Tool
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  • Timeline
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  • Workplace
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Optional plug-ins will be packaged as = features and will be posted to an update site on the i2b2 web page. Users w= ill have the ability to easily add features (optional plug-ins) from within= the i2b2 workbench by going to the help menu and selecting Add new feature= s.

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Tooltips E= nhanced (Navigate Terms)

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The tooltips that appear in Navigate Terms view have been enhanced to al= low users to select whether or not they want to display the concept code in= the tooltip and/or use the short tooltip.

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Analysis View

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A new Analysis view has been created that will allow users to view a bre= akdown of the data in a bar chart.
Detailed information regarding the f= unctionality of the Analysis plug-in and view can be found in the Analysis = documentation included in this release.
Provided below is an outline of= some key features of the Analysis View.

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  1. Breakdown of patients by Age, Gender, Race and Vital Status.
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  3. Able to save an image of the graph showing the breakdown.
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Export Data View

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The new export data view will enable users to export data from one of th= e following tables.

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Detailed information regarding the fun= ctionality will be provided in other documentation.

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Note: This new view is an optional plug-in which can be added using the n= ew "features" enhancement.

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Replacement of Gri= dsphere

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In version 1.4 the gridsphere is replaced with an admin component in the= i2b2 Web Client.
Detailed information regarding the functionality of t= he replacement of the gridsphere and changes to the PM services can be foun= d in one of the following documents.

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  1. PM_design_1-4 (will be included in a future release candidate)=
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  3. PM_Installation_1-4.pdf
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  5. PM_Messaging_1-4.pdf
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Roles Based Access

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Roles based access has been added to the i2b2 Workbench. Users will be a= llowed to perform specific tasks based upon their associated role. For inst= ance, only users who have the role of DATA_DEID will be able to see de-iden= tified data.
Detailed information regarding the functionality of roles = based access can be found in the PM design documentation which will be prov= ided in an upcoming release candidate.
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Active Directo= ry Service (ADS)

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In the new admin tool (PM) users can now choose whether or not they want= to use ADS to authenticate against the active directory.
Detailed info= rmation regarding the ADS can be found in the PM design documentation which= will be provided in an upcoming release candidate.

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Server Side Plug-in

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A plug-in on the server has been added that will assist users in setting= up custom plug-ins to work with the CRC.
Detailed information regardin= g the functionality of the new server side plug-in can be found in one of t= he following documents:

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  1. CRC Architecture_1.4.pdf
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  3. CRC Installation_1.4.pdf
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  5. CRC Message_1.4.pdf
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Analysis Break= down in Ontology

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Users will be able to view an analysis breakdown of the concepts in Onto= logy by toggling on/off the count in Navigate Terms View.
Detailed info= rmation regarding the functionality of the new server side plug-in can be f= ound in one of the following documents:

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  1. Ontology Architecture_1.4.pdf
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  3. Ontology Installation_1.4.pdf
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  5. Ontology Message_1.4.pdf
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Obfuscation

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The roles that are given to a user may determine that they are only allo= wed to view obfuscated (statistically anonymized) data. The patient counts = that are returned to the client no longer represent true counts, but are "b= lurred" by a random amount. If the same query is performed multiple times (= perhaps to average the blurring effect) the patient is locked out of the sy= stem.

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Paging

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The XML representing the patient data object (PDO) may be very large in = some types of requests. If the server determines that the entire PDO cannot= be served back due to resource limitations on the server-side, the server = returns the largest number of patients it can satisfy, and information for = the client to page through the remaining requests is included in the respon= se.

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Updates

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Documentation:

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The 1.4 release documentation can be found in a zip file located on the = i2b2 web page. This file includes documentation for the following:

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Fixes:

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The following fixes were added to this release.

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Query with text value constraint returns zero patients

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Zero patients will be returned when you run a query in which one of the = concepts has a value constraint associated to one of the concepts. This pro= blem only occurs if the type of value is a text value like "POSITIVE", "NEG= ATIVE", "1+", "FEW", etc.. Queries will run correctly if the type of value = is numerical or if the constraint is based on a flag such as "HIGH" or "LOW= ".
STATUS/RESOLUTION: This issue has been resolved= . All queries now return the appropriate patients.

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PM: Parameters ar= e not saved

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New parameters entered via Admin in the web client are not being saved t= o the database. This is happening for all parameters (Project, User, etc).<= br> STATUS/RESOLUTION: This issue has been resolved. U= sers can now save parameters.

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PM: Not= all project information is saved

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The "Project Description" and "Project Path" are not saved when entering= a new project or editing an existing one.
STATUS/RESOLUTION: This issue has been resolved. Project description and path are = now saved.

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PM:= Project key changes when saving a project

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A new "Project Key" is assigned every time you save an edit to the proje= ct. This is a primary key and should not be edited.
STATUS/RESO= LUTION: This issue has been resolved. Edits to a project no lo= nger change the key.

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PM: Pr= oject user roles only saves one role

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When associating a user to a project you can select multiple roles. The = problem is only one role is being saved even though several have been selec= ted.
STATUS/RESOLUTION: This issue has been resolv= ed. Multiple roles can now be saved for a user.

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Licensing

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The i2b2 source code is licensed under the i2b2 Software License 2.1. Th= is includes but is not limited to all code in the edu.harvard.i2b2.* packag= e namespace.

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Trademarks

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Microsoft, Windows, Windows XP, Windows Vista, Windows 7 and Windows Ser= ver are either registered trademarks or trademarks of Microsoft Corporation= in the United States and/or other countries.

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Mac OS is a registered trademark of Apple, Inc.

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Eclipse Galileo is a registered trademark of the Eclipse Foundation, Inc= .

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All other trademarks are the property of their respective owners.

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