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This release note applies to you if you are upgrading to 1.6.0030 from a computer running an earlier version of the i2b2 workbench. This release contains client, server and database changes so it is important to update all.
If you are installing 1.6.0030 from a computer running the i2b2 workbench, ensure that the workbench and all eclipse applications are closed prior to installing this release.
WHERE DO I START?
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 documentation folder.

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The YUI, which is used by the i2b2 Web Client, was upgraded to version 2.8.2
Information about YUI can be found on the YUI Library website (http://developer.yahoo.com/yui)

New Features

i2b2 release 1.6.0030 contains new features that have been outlined below.

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  • When a query is requested to run and it is constrained by the "Same Financial Encounter", the data will be tied together by the encounter_num and positive "hits" will only yield patients who have these observation_facts occurring together in one of their visits.
  • When a query is requested to run and it is constrained by the "Instance will be the same", the data will be tied together by the encounter_num and instance_num; positive "hits" will only yield patients who have these observation_facts occurring together in same instance of their visit.


  • In addition to the encounter_num and instance_num matching the following additional columns have to match in order to be considered the "same instance" patient_num, concept_cd, start_date, and provider_id


This similar logic is applied to the panel timing. The main difference being that the timing is defined for each individual panel as opposed to the entire query.
To avoid confusion the following outlines the labels seen in the client and the associated timing of any or same.

Timing Level
(Query or Panel)

Label in Client

Timing
(ANY or SAME)

*** Query Timing

Treat all groups independently

ANY

*** Query Timing

Selected groups occur in the same financial encounter

SAME

Panel Timing

Treat Independently

ANY

Panel Timing

Occurs in Same Encounter

SAME


*** In the web client "Query Timing" is called "Temporal Constraint". Although they are labeled differently the functionality is the same.
Example 1:
Patient has a medication with a dose greater than 500 mg and a medication that is taken once a day documented at any time in their history.
 
 
RESULTS: there are 47 patients who have had a medication with a dose greater than 500 mg and a frequency of once a day entered as a fact in the observation_fact table, where the medication dose and frequency have the same patient_num.
 Example 2:
Patient has a diagnosis of Acute MI documented at any time in their history and they have a medication with a dose greater than 500 mg and a medication that is taken once a day documented during the same visit.

 RESULTS: there are 4 patients who have had a medication with a dose greater than 500 mg and a frequency of once a day entered as a fact in the observation_fact table, where the medication dose and frequency have the same encounter_num AND the diagnosis of acute MI, the medication dose and frequency all have the same patient_num.
Example 3:
Patient has a diagnosis of Acute MI documented at any time in their history and they have a medication with a dose greater than 500 mg and a medication that is taken once a day documented during the same instance.

RESULTS: there are 3 patients who have had a medication with a dose greater than 500 mg and a frequency of once a day entered as a fact in the observation_fact table, where the medication dose and frequency have the same encounter_num AND instance_num AND the diagnosis of acute MI, the medication dose and frequency all have the same patient_num.
 

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The ability to track and display performance metrics when running a query has been added to 1.6 Release. The tracking information can be turned on by setting the following project parameter.
Parameter Name: PM_ENABLE_PROCESS_TIMING
Parameter Value: DEBUG
When the performance tracking is turned on (set to DEBUG) the information will appear in the Query Status view when you run the query.

  • This change is only available in the i2b2 Web Client.


Update Term Usage Utility

In the 1.6 Release a new utility has been added to the i2b2 Workbench. This new utility enables users to easily run an update process which will update each term with the total number of times the term is used in the observation_fact table.
These totals can be seen in the Navigate Terms view by turning on the "Enable patient counts" in the Options dialog. This also enables performance tuning by the query engine.

  • This view is available in the workbench and the process can only be run by a user who has the role of "Editor" associated to them.


Ontology View - Updates to Options Dialog

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  • A medication can be modified with the dose, route, and frequency.
  • A procedure can be modified with a CPT modifier(s) indicating a two surgeon team with anesthesia by anesthesiologist (62 and AA).
  • A diagnosis involving malignant neoplasms can be modified with the TNM staging information.
  • Allergies and other diagnoses can be modified with the severity.


  • The changes made to the database to support modifiers are listed in the Update section under Data


Unit Conversion

In the 1.6 Release the ability to run queries using units other than the normal unit has been added. This feature is beneficial for those numerical facts that are not stored in normalized unit_cd.
The user can enable the unit conversion process by setting the following Project Parameter.
Parameter Name: CRC_ENABLE_UNITCD_CONVERSION
Parameter Value: ON

  • This unit conversion option will slow the query, so for better query performance load the numerical fact values in the normalized units and do not enable this option.


When the above parameter is set to 'ON', the unit conversion of the nval_num is calculated using the concept's metadata xml defined in the ontology cell (<ConvertingUnits/> , <MultiplyingFactor/>). The unit conversion in the query is done before applying the value constraint.

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It is important to note that when excluding a modifier term the table will contain multiple entries for that modifier.
The following is a snippet from the i2b2 metadata table. In this example, the modifier term called Severity: Mild will be applied to the Diagnoses concept and all its children EXCEPT for the following two concepts and all their children. (1) Neoplasms and (2) Mental Disorders

  • This snipped only includes those columns that are relevant to the example.


C_FULLNAME

C_NAME

M_APPLIED_PATH

M_EXCLUSION_CD

\Severity\Mild\

Severity: Mild

\i2b2\Diagnoses%

NULL

\Severity\Mild\

Severity: Mild

\i2b2\Diagnoses\Neoplasms (140-239)%

X

\Severity\Mild\

Severity: Mild

\i2b2\Diagnoses\Mental Disorders (290-319)%

X

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When a query "times out" a response message is filed in the JMS queue. These response messages are never cleared out of the queue. This can result in apparent prolonged response times.
STATUS/RESOLUTION: This issue has been resolved. Query response messages will now be removed from the queue.

The following outlines how to fix this issue in an existing system.
Edit File: JBOSS_HOME/server/default/deploycrc-queryresponse-q-service.xml
Update lines:
<attribute name="RedeliveryLimit">1</attribute>
<attribute name="RedeliveryDelay">1</attribute>

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