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From: Peter Beninato [beninato.ohsu] Sent: Friday, March 30, 2012 6:24 PM To: Peter Beninato; i2b2 AUG Member Subject: RE: i2b2 - v1.6.03 - Query Status - Less than 10... continued... --> solved
Hi,
So, when a query is run, the information in the Query Status window is served up by, private_refresh_status(),  in CRC_ctrlr_QryStatus.js. Here is a snippet that reflects the change:

                                                                                for (var i2 = 0; i2 < params.length; i2++) {
                                                                                                var name = params[i2].getAttribute("name");
                                                                                                if (i2b2.PM.model.isObfuscated) {
                                                                                                                if ( params[i2].firstChild.nodeValue < 10) {
                                                                                                                                var value = "Less than 10";          
                                                                                                                } else {
                                                                                                                                var value = params[i2].firstChild.nodeValue + "±3" ;
                                                                                                                }
                                                                                                } else
                                                                                                {
                                                                                                                if ( params[i2].firstChild.nodeValue < 10) {
                                                                                                                    var value = "Less than 10";
                                                                                                                }
                                                                                                                else {
                                                                                                                    var value = params[i2].firstChild.nodeValue;
                                                                                                                }                                                                             
                                                                                                }
                                                                                                self.dispDIV.innerHTML += "<div style=\"clear: both; margin-left: 20px; float: left; height: 16px; line-height: 16px;\">" + params[i2].getAttribute("column") + ": <font color=\"#0000dd\">" + value  + "</font></div>";
                                                                                }

However, when you drag and drop a Previous Query the CRC cell, the Query Status is update by laodQueryStatus() in CRC_ctrlr_QryTool.js. Here is snippet:
                                                                                for (var i2 = 0; i2 < params.length; i2++) {
                                                                                                var name = params[i2].getAttribute("name");
                                                                                //            $('infoQueryStatusText').innerHTML += "<div style=\"margin-left: 20px; clear: both; height: 16px; line-height: 16px;\">";
                                                                                //            $('infoQueryStatusText').innerHTML += "<div style=\"clear: both; margin-left: 20px; float: left; height: 16px; line-height: 16px;\">" + params[i2].getAttribute("column") +  ": <font color=\"#0000dd\">" + params[i2].firstChild.nodeValue + "" +  (i2b2.PM.model.userRoles.indexOf("DATA_LDS") == -1 ? "±3" : "")  +   "</font></div>";
                                                                                                $('infoQueryStatusText').innerHTML += "<div style=\"clear: both; margin-left: 20px; float: left; height: 16px; line-height: 16px;\">" + params[i2].getAttribute("column") +  ": <font color=\"#0000dd\">" + (params[i2].firstChild.nodeValue > 10 ? params[i2].firstChild.nodeValue : " Less than 10") + "" +  (i2b2.PM.model.userRoles.indexOf("DATA_LDS") == -1 ? "±3" : "")  +   "</font></div>";
                                                                                //$('infoQueryStatusText').innerHTML += "</div>";                                                                                        //i2b2.h.XPath(newxml, 'descendant-or-self::result/data')[0].firstChild.nodeValue;
                                                                                }

From: Peter Beninato [[beninato.ohsu]|mailto:beninato@ohsu.edu] Sent: Thursday, March 29, 2012 4:44 PM To: i2b2 AUG Member Subject: i2b2 - v1.6.03 - Query Status - Less than 10... continued...


Hi,
Well...
I got the Prevous Queries section to show "Less than 10" by editing CRC_sdx_QI.js Yay!
However, despite editing CRC_ctrlr_QryStatus.js in the method, _GetTitle, and ensuring that the js is refreshed and updated via the browser.
I don't see any difference. I even took the step of removing the conditional (IF clause) around the two calls to this method in the script.
But still I don't see any difference.
Is the patient record count in the Query Status really served up by CRC_ctrlr_QryStatus.js?
Thx.

Peter Beninato
OCTRI DW Developer
Oregon Health & Science University


NEXT EMAIL
From: Peter Beninato [beninato.ohsu] Sent: Thursday, March 29, 2012 4:04 PM To: Peter Beninato; i2b2 AUG Member Subject: RE: i2b2 - v1.6.03 - Less than 10 - Query Status , Previous Query
Hi,
I think problem is related to caching in browser.
If I can't resolve, I make another post.
Fyi.

From: Peter Beninato [[beninato.ohsu]|mailto:beninato@ohsu.edu] Sent: Thursday, March 29, 2012 11:31 AM To: i2b2 AUG Member Subject: i2b2 - v1.6.03 - Less than 10 - Query Status , Previous Query


Hi,
I have a system requirement that I got to work in version 1.4, which is when the count is Less than 10, show "Less than 10" and am trying to replicate in v1.6.03.
In the past I edited these two files:
CRC_ctrlr_QryStatus.js
CRC_sdx_QI.js

In the past I did an edit like:
o.title = "Less than 10 patients";

However, What I'm seeing for an obfuscated user, in the query status, when the count is less than 10 is
patient_count 7 +/- 3
I want to show "Less than 10"
Both in the Previous Query and Query Status panels, How do I change the titles for counts?
Here is the edit I have going in CRC_ctrlr_QryStatus.js which is not working...
Thanks.
                                case "PATIENT_COUNT_XML":
                                                // use given title if it exist otherwise generate a title
                                                try {
                                                                var t = i2b2.h.XPath(oXML,'self::query_result_instance/description')[0].firstChild.nodeValue;
                                                } catch(e) {
                                                                var t = null;
                                                }
                                                if (!t) { t="Patient Count"; }
                                                // create the title using shrine setting
                                                if (oRecord.size >= 10) {
                                                                if (i2b2.PM.model.isObfuscated) {
                                                                                //title = t+" - "oRecord.size"±3 patients";
                                                                                title = t;
                                                                } else {
                                                                                title = t+" - "oRecord.size" patients";
                                                                }
                                                } else {
                                                    title = "Less than 10 patients";
                                                                //if (i2b2.PM.model.isObfuscated) {
                                                                //            title = t+" - 10 patients or less";
                                                                //} else {
                                                                //            title = t+" - "oRecord.size" patients";
                                                                //}
                                                }
                                                break;

Peter Beninato
OCTRI DW Developer
Oregon Health & Science University


NEXT EMAIL
From:Murphy, Shawn N.
Sent:Friday, March 23, 2012 7:50 AM
To: Sebastian Mate; i2b2 AUG Members
Subject:RE: New i2b2 Wizard for 1.6.03 with TNS bugfix
Thanks Sebastian, this Wizard is a great contribution. Shawn.

From: Sebastian Mate [Sebastian.Mate.imi.med.uni-erlangen.de]
Sent: Thursday, March 22, 2012 11:33 AM
To: i2b2 AUG Members
Subject: New i2b2 Wizard for 1.6.03 with TNS bugfix
Hi all,
I have created a new i2b2 Wizard to support i2b2 1.6.03.
It also includes a messy workaround (it's not a true fix) for the ORA?12519 TNS issue that we've discussed recently. It automatically applies the Oracle database setting to increase the concurrent database connections and restarts the Oracle database whenever the JBoss process is being restarted through i2b2 Wizard.
The new version is 1.3.6 and can be found here: http://www.imi.med.uni?erlangen.de/~matesn/i2b2wizard/
Cheers
Sebastian
Dipl.?Inf. Sebastian Mate (computer scientist) Friedrich?Alexander?University of Erlangen Nuremberg Department for Medical Informatics
Krankenhausstrasse 12, 91054 ERLANGEN, GERMANY Phone +49 9131/85?26785, Fax +49 9131/85?26754
Sebastian.Mate.imi.med.uni?erlangen.de http://www.imi.med.uni?erlangen.de



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From: Peter Beninato [beninato.ohsu]
Sent:Thursday, March 22, 2012 1:51 PM
To: i2b2 AUG Members
Subject:i2b2 - v1.6.03 - metadata - upgrade scripts
Hi,
I'm examining the upgrade scripts for changes. In v.1.6.02, there were statements like:
ALTER TABLE I2B2
ADD (m_applied_path varchar2(700) DEFAULT '@' NOT NULL...
Now there is: ALTER TABLE I2B2
ADD (m_applied_path varchar2(700) NULL...
Then followed with an UPDATE: UPDATE I2B2
SET m_applied_path = '@'

Is the intent that any NULL value for m_applied_path should be the "@" sign?
If so, the approach utilized for v1.6.02 might be preferable, since, in production systems the i2b2 table (custom_meta etc.) are often truncated, and reloaded.
The DEFAULT value approach used in v1.6.02 ensures that an "@" is inserted, whereas, the approach in v1.6.03 relies on a business rule being applied during ETL, and the need for an "@" as a null?type value might be overlooked.

Peter Beninato - OCTRI DW Developer
Oregon Health & Science University
503-494-9985 beninato.ohsu



NEXT EMAIL
From: Daniele Segagni [daniele.segagni.fsm.it]
Sent:Thursday, March 22, 2012 8:59 AM
To:Murphy, Shawn N.
Cc:i2b2 members
Subject:Re: ontology modifier question
Thank you Shawn for your exhaustive answer with which we have better understood the use of modifiers.
Thanks, Daniele
Ing. Daniele Segagni
Laboratorio di Informatica e Sistemistica per la Ricerca Clinica
IRCCS Fondazione S.Maugeri, Pavia, Italy tel: +39 0382 592038

Murphy, Shawn N. ha scritto:
Hi Daniele,
Modifiers do give more choices for how to represent the data. In some cases it is probably a good idea to represent a value with a modifier, like the dose of a medication. But overall I would recommend using modifiers sparingly, they increase the complexity of the ontology model and are harder on the user doing queries to conceptualize.
For age you could definitely use it with a value, and I think several i2b2 sites do represent it that way. We put it in the ontology discretely just as a choice. You can see in the demo data that we tie it to SQL queries that query for the age dynamically so to obtain their current age from the birth_date column of the patient_dimension.
Thanks,
Shawn.

From: Daniele Segagni [daniele.segagni.fsm.it]
Sent: Thursday, March 22, 2012 5:58 AM
To: i2b2 members
Subject: ontology modifier question
Hi all,
our team in Pavia (italy) is moving to version 1.6.03 and we're structuring the ontology using modifiers. Watching the metadata in the 1.6.03 ontology database and the i2b2 wiki document titled "Modifiers in i2b2 Data Model" we show that modifiers are not used for fields with continuous value, such as Demographic - Age / Visit - Length of stay. Is there a specific reason for that choice?
We've supposed to use them like this:
"Value" as modifier of the leaf "Age"
where the modifier has specified in the c_metadataxml field
<Datatype>PosInteger</Datatype>.
In this way when the "Value" modifier is dragged in the Query tool, the user could use the dialog box to select the range of values.
Any advice or comment on this?
Thank you,
Daniele
Ing. Daniele Segagni
Laboratorio di Informatica e Sistemistica per la Ricerca Clinica IRCCS
Fondazione S.Maugeri, Pavia, Italy
tel: +39 0382 592038



NEXT EMAIL
From: Sebastian Mate [Sebastian.Mate.imi.med.uni-erlangen.de]
Sent:Monday, March 19, 2012 5:44 AM
To:'Daniele Segagni'
Cc: Mendis, Michael E.; i2b2 AUG Members
Subject:AW: AW: AW: ORA-12519, TNS:no appropriate service handler found
Hi Daniele,
this is cool, thanks a lot.
Maybe we could implement something that monitors this value and restarts the i2b2 server, if necessary. However, it would be better if this gets fixed in the i2b2 source code. Anyway, an i2b2 "watchdog" (that permanently monitors the i2b2 server) is something I had in mind for quite some time
Regards
Sebastian

Von: members+bncCJnupqLOBxDc_Jv7BBoEL8HvpA.i2b2aug[ [members+bncCJnupqLOBxDc_Jv7BBoEL8HvpA.i2b2aug] |mailto:members%2BbncCJnupqLOBxDc_Jv7BBoEL8HvpA@i2b2aug.org]Im Auftrag von Daniele Segagni Gesendet: Montag, 19. März 2012 10:35
An: Sebastian Mate
Cc: 'Mendis, Michael E.'; i2b2 AUG Members
Betreff: Re: AW: AW: ORA-12519, TNS:no appropriate service handler found
Hi Sebastian,
you are certainly right, I also suspect that some connections remain open. However, if you want to monitor your Oracle instance processes you can use this script:
SELECT sess.process, sess.status, sess.username, sess.schemaname, sql.sql_text
FROM v$session sess, v$sqlsql
WHERE sql.sql_id(plus) = sess.sql_id
AND sess.type= 'USER'
The outer join is to handle those sessions that aren't currently active. Regards,
Daniele
Ing. Daniele Segagni
Laboratorio di Informatica e Sistemistica per la Ricerca Clinica
IRCCS Fondazione S.Maugeri, Pavia, Italy tel: +39 0382 592038

Sebastian Mate ha scritto:
Hi Daniele,
thanks a lot! (I will integrate this into the next i2b2-Wizard.)
However, are we sure that i2b2 does not exceed 300 connections? What makes
me wonder is even with the default setting, it is working fine for a certain
time before it starts to go crazy. Since waiting doesn't solve the problem, I assume that i2b2 doesn't close some connections ...
Regards
Sebastian

Von: members+bncCJnupqLOBxCy8Zv7BBoEtvQp3w.i2b2aug [members+bncCJnupqLOBxCy8Zv7BBoEtvQp3w.i2b2aug] Im Auftrag von Daniele Segagni
Gesendet: Montag, 19. März 2012 10:11
An: Mendis, Michael E.
Cc: Sebastian Mate; <i2b2 AUG Members>
Betreff: Re: AW: ORA-12519, TNS:no appropriate service handler found
Hi Mike and Sebastian,
after several attempts I tried the db script send by Mike and it seems to work fine. The scrip slightly modified is:
select * from gv$resource_limit;
alter system set processes=300 scope=spfile;
Reboot the database to let parameter taking effect. Regards,
Daniele
Ing. Daniele Segagni
Laboratorio di Informatica e Sistemistica per la Ricerca Clinica
IRCCS Fondazione S.Maugeri, Pavia, Italy tel: +39 0382 592038

Mendis, Michael E. ha scritto:
so you are running oracle (sun) java and not openjdk?(of course if I
read your original email I could realize that you are using the VM image) (-;
First try to see what you are currently set at for number of processes show parameter process
Try to increase the process parameters on oracle with the following: ALTER SYSTEM SET PROCESSES=150 SCOPE=SPFILE

On Mar 16, 2012, at 9:47 AM, Daniele Segagni wrote: My java version is 1.0.6_16
Ing. Daniele Segagni
Laboratorio di Informatica e Sistemistica per la Ricerca Clinica
IRCCS Fondazione S.Maugeri, Pavia, Italy tel: +39 0382 592038

Mendis, Michael E. ha scritto:
Daniele,
What version of java are you running?
mike

On Mar 16, 2012, at 9:22 AM, Daniele Segagni wrote:
We are testing our data warehouse using the i2b2 1.6.02 VM downloaded from the i2b2.org<http://i2b2.org> website (on this VM we changed only the Jboss
Data Source files in order to use our Oracle server).
Our errors are like yours, related only to the CRC connection while ONT and WORK continue to work fine.

Regards
Ing. Daniele Segagni
Laboratorio di Informatica e Sistemistica per la Ricerca Clinica
IRCCS Fondazione S.Maugeri, Pavia, Italy
tel: +39 0382 592038

Sebastian Mate ha scritto:
Hi Mike,
it appears to happen after a certain up-time or a certain number of queries.
It only affects the CRC cell, which does no longer work after the error appears. ONT and WORK seem to continue to work.

Hi Daniele,
which Java version are you using?
I also have to mention that our installation is an "i2b2 Wizard"-based one (Ubuntu 10.04) which makes use of OpenJDK. I think the error appeared first when we had to switch to OpenJDK.
I will continue to investigate on this error ...
Regards
Sebastian

Von:
[members+bncCLO22I_kHRCK8Iz7BBoEOx6aWw.i2b2aug] Im Auftrag von
Mendis, Michael E.
Gesendet: Freitag, 16. März 2012 13:54
An: Sebastian Mate; i2b2 AUG Members<i2b2 AUG Members> Betreff: RE: ORA-12519, TNS:no appropriate service handler found
Not sure about openjdk, but I know of someone who had issues with GnuJava
Was this error all the time or just sometimes?
mike

From: Sebastian Mate
[Sebastian.Mate.imi.med.uni-erlangen.de<Sebastian.Mate.imi.med.uni-er langen.de>]
Sent: Friday, March 16, 2012 8:04 AM
To: i2b2 AUG Members<i2b2 AUG Members>
Subject: ORA-12519, TNS:no appropriate service handler found
Hi all,
I'm noticing „ORA-12519, TNS:no appropriate service handler found" errors in
i2b2 1.6.02.
I'm not sure if this is because of i2b2 1.6.02 or the fact that I'm using
OpenJDK (Oracle Java was removed from Ubuntu).
According to
http://www.synchrosinteractive/blog/1-software/75-oracle-xe-on-ubuntu-11
04-32-bit this error could be caused by too many open database connections.
I will try to increase this number. But if it helps, it seems to be a bug of the i2b2 server, which doesn't close its connections ... Has anyone else noticed this strange error?
Kind regards
Sebastian
Dipl.-Inf. Sebastian Mate (computer scientist)
Friedrich-Alexander-University of Erlangen Nuremberg Department for Medical
Informatics Krankenhausstrasse 12, 91054 ERLANGEN, GERMANY Phone +49
9131/85-26785, Fax +49 9131/85-26754



NEXT EMAIL
From:Mendis, Michael E.
Sent:Friday, March 16, 2012 2:18 PM
To:Harris, Daniel R
Cc: <i2b2 AUG Members>
Subject:Re: 1.603 upgrade notes
Daniel,
This will enable data_lds get text from the blobs, might want to set it to data_deid. I did check out install and upgrade scripts and did see the insert for this in them. Thanks for the info that if it is missing the crc does not function, in the next version will address this and also that having duplicate entries, the crc will throw an exception that 2 entries found and one was expected.
thanks mike

On Mar 16, 2012, at 12:54 PM, Harris, Daniel R wrote:
Dear all,
We updated from 1.602 to 1.603 by re-deploying the hive cells.
Although there are no structural changes to the DBs, QT_PRIVILEGE will need to be updated to contain SETFINDER_QRY_WITH_LGTEXT with the appropriate permission for your institution. Without this, i2b2 will fail when obtaining permissions.
Below is a simple SQL statement (we use sql-server) that might help your upgrade process:
insert into i2b2data.dbo.[QT_PRIVILEGE] (PROTECTION_LABEL_CD, DATAPROT_CD, HIVEMGMT_CD)
VALUES ('SETFINDER_QRY_WITH_LGTEXT', 'DATA_LDS', 'USER')
Thanks,
Daniel Harris
University of Kentucky
Department of Computer Science and
Division of Biomedical Informatics
182 BioPharm Complex Building
789 South Limestone Street
Lexington, Kentucky 40536-0596



NEXT EMAIL
From: Daniele Segagni [daniele.segagni.fsm.it]
Sent:Friday, March 16, 2012 9:07 AM
To:Sebastian Mate
Cc: i2b2 AUG Members
Subject:Re: ORA-12519, TNS:no appropriate service handler found
Hi Sebastian,
we in Pavia (Italy) also found the same type of error. We are monitoring the Oracle connections to verify if all are properly closed, but i someone have just found a good solution we would like to try it.
Regards
Daniele
Ing. Daniele Segagni
Laboratorio di Informatica e Sistemistica per la Ricerca Clinica
IRCCS Fondazione S.Maugeri, Pavia, Italy tel: +39 0382 592038

Sebastian Mate ha scritto:
Hi all,
I'm noticing „ORA?12519, TNS:no appropriate service handler found" errors in i2b2 1.6.02.
I'm not sure if this is because of i2b2 1.6.02 or the fact that I'm using OpenJDK (Oracle Java was removed from Ubuntu). According to http://www.synchrosinteractive/blog/1?software/75?oracle?xe?on?ubuntu?1104?32?bit this error could be caused by too many open database connections. I will try to increase this number. But if it helps, it seems to be a bug of the i2b2 server, which doesn't close its connections ... Has anyone else noticed this strange error?
Kind regards
Sebastian
Dipl.?Inf. Sebastian Mate (computer scientist) Friedrich?Alexander?University of Erlangen Nuremberg Department for Medical Informatics
Krankenhausstrasse 12, 91054 ERLANGEN, GERMANY
Phone +49 9131/85?26785, Fax +49 9131/85?26754
Sebastian.Mate.imi.med.uni?erlangen.de http://www.imi.med.uni?erlangen.de



NEXT EMAIL
From:Murphy, Shawn N.
Sent:Thursday, March 15, 2012 10:57 PM
To: i2b2 AUG Members
Subject:i2b2 1.6.03 is released
New Features:
Large Text Searches
In the previous release, 1.6.02 we introduced a new feature called "String Constraints". Basically a string search ("constraint") is similar to other value constraints in that users can narrow down their search criteria based on a small string of text stored in the tval_char column of the observation_fact table. (For more information on string constraints see the notes for Release 1.6.02).
In release 1.6.03 we now introduce the ability to narrow down your search based on text that is stored in the observation_blob column of the observation_fact table. This new feature is called "Large Text Searches" as the data that is stored in this column is typically a large blob of text such as a report.
To the user the process defining a text search, whether it is a "small string" or "large text string" is pretty straight forward and similar. There are a few minor differences they will see. For example:
Small string search users can define the value operator (example; contains, starts with, ends with, and exact). Large text string search works similar to other search engines; Specifically users can define database search operators in the string of text they enter.
The metadataxml defined for the concept or modifier will determine which value constraint window will display to the user. The metadataxml will also determine the <value_type> that is sent in the xml request message. This <value_type> will define whether or not the tval_char or the observation_blob column is searched for the defined text.
WEB CLIENT: Auto?generate "Timeline"
In the past, when running a query with the result type of Timeline selected it would simply return a patient set. In 1.6.03 this feature has been updated so that now when it is selected, the timeline plug?in will open and automatically display the results in the timeline (if user permissions allow). This feature is already available in the i2b2 Workbench (eclipse client) so this change is to add it to the web client.
WEB CLIENT: View text (reports) in the timeline
In 1.6.03 users can now view text (reports) from within the timeline. When double clicking on the tick mark that appears for the report a new window will open displaying the text. This feature is already available in the i2b2 Workbench (eclipse client) so this change is to add it to the web client.
Currently encrypted notes are not supported and cannot be viewed in the timeline plug?in for the web client. They can be viewed in the i2b2 workbench (eclipse client) with the appropriate encryption key.
WEB CLIENT: Print Query added to Query Status
The option to print a query has been added to the Query Status view of the Web Client. A new icon appears in the top right corner of the Query Status view. A new window will open when you click on this icon. In this window all the information regarding the query and it constraints will appear in the header of the document. The results returned will appear below the header in the body of the report.
Thanks,
Shawn, Mike, Raj, Lori, Wensong, and Janice.



NEXT EMAIL
From: Dat Q. Phan [Dat.Q.Phan.uth.tmc] Sent:Wednesday, March 14, 2012 11:18 AM To:Brian Ostasiewski
Cc: i2b2 AUG Members; Phillip Reeder
Subject:RE: String Index Out of Range Error
Thanks Brian for the suggestion. We resolved this. Turns out 1.5.5 didn't like how we were referencing other tables besides the concept_dimension table in our terminology table.
Johnny

From: Brian Ostasiewski [bostasie.wakehealth]
Sent: Wednesday, March 14, 2012 6:38 AM
To: Dat Q. Phan
Subject: RE: String Index Out of Range Error
Check your concept paths that you're querying – I think the bug with odd characters may have been fixed in 1.6.01 and could still be in 1.5.5. Look for a apostrophes or extended ascii chars .

From: Dat Q. Phan [Dat.Q.Phan.uth.tmc]
Sent: Tuesday, March 13, 2012 6:53 PM
To: i2b2 AUG Members
Cc: Phillip Reeder
Subject: String Index Out of Range Error
Hi,
I'm getting an error whenever I run a query on i2b2 v1.5.5.
ERROR [STDERR] java.lang.StringIndexOutOfBoundsException: String index out of range: ?1
I don't get this error with the demo data but I do with our patient data but I'm not sure where this error is coming from. Has anyone encountered this? Any help would be appreciated.
Thanks,
Johnny Phan Programmer Analyst II UTHealth
School of Biomedical Informatics
Dat.Q.Phan.uth.tmc



NEXT EMAIL
From: Lisa Miao [lmiao.regenstrief]
Sent:Tuesday, March 13, 2012 3:28 PM
To: Murphy, Shawn N.; i2b2 AUG Members
Subject:RE: drug data
Thanks Shawn for writing back, and thanks everyone for sharing their experiences.
Do we have a medication hierarchy defined? Matvey Palchuk shared his paper at AMIA. The main idea is to create a hierarchical view of RxNorm using NDF?RT drug class definition. I've been told this is what SHRINE has adopted. Has this become the most endorsed standard?
We are using NDC codes for medication. RxNorm to NDC mapping is readily available. We certainly like to find out if the
NDF?RT/RxNorm is going to become the standard for defining medication hierarchy. Thanks,
Lisa.

From: Murphy, Shawn N. [SNMURPHY.PARTNERS]
Sent: Tuesday, March 13, 2012 1:13 PM To: Lisa Miao; i2b2 AUG Members Subject: RE: drug data
Hi Lisa,
In general, in an operational setting, our mapping exercise is a data driven problem. The medication codes that need to be mapped into a medication hierarchy depend on what we see in the local data. This will define how many codes we need to map into the base hierarchy. The NDC codes that are mapped into the medication hierarchy in the demo ontology are an example of how local codes such as these can be mapped into the base ontology.
We'll be presenting some new tools that are being developed with the NCBO at the AMIA summit next week that help take a list of local codes and map them into a base hierarchy.
Thanks, Shawn.

From: Lisa Miao [lmiao.regenstrief]
Sent: Monday, March 12, 2012 10:41 AM
To: i2b2 AUG Members
Subject: drug data
Dear all,
Has anyone successfully loaded patient drug data into i2b2? I would greatly appreciate if anyone can share some experience.
The issues that we encountered are, what drug codes should be used? I wouldn't think NDC codes are practical, since there are over 800k NDC codes, and they are continuing to develop. The i2b2demodata does have NDC codes, I suspect it's a subset, because having 800k to the term tree isn't going to be practical. Could i2b2 team comment on this?
I've tried to load RxNorm codes into the term tree. Trouble is there isn't a good tree structures for RxNorm codes. The second level (which I think are all the ingredients) have about 5000 ingredients. When I put them into i2b2, and try to expand, the webclient isn't able to expand the tree. I would assume it's because of the number of nodes.
Anyone has any experiences? Thanks,



NEXT EMAIL
From: Nathan Graham [ngraham.kumc]
Sent:Tuesday, March 13, 2012 9:44 AM
To: i2b2 AUG Members; Churchill, Susanne E.
Subject:i2b2 Academic Users' Group
Hello,
I just started work in the Department of Biostatistics at Kansas University Medical Center under the direction of Professor
Russ Waitman. As I began learning about i2b2 and related topics, he suggested that I join the i2b2 academic user group. The i2b2 AUG website says to contact you if interested in joining.
Thanks! Regards, Nathan
Nathan Graham Software Engineer Department of Biostatistics
University of Kansas Medical Center ngraham.kumc http://informatics.kumc



NEXT EMAIL
From: McMurry, Andrew J. [Andrew\_McMurry.hms.harvard\] (mailto:_McMurry@hms.harvard.edu)
Sent:Monday, March 12, 2012 2:32 PM
To:Law, James
Cc: Lisa Miao; i2b2 AUG Members
Subject:Re: drug data

In SHRINE, we mapped to RxNorm with the NDF-RT hierarchy https://open.med.harvard.edu/display/SHRINE/Core+Ontology
Hope this helps,
andy

On Mar 12, 2012, at 11:54 AM, Law, James wrote:
Lisa,
Most of our research related data requests do not seem to contain selection criteria concerned with drug dose forms, route, or even a specific brand. Therefore we created an ontology based on a unique set of ingredients in the drug as our concept cd in concept dimension. We then use our drug database(First Data Bank---FDB) to map each med to its respective unique ingredient id. The end result is that if an end user selects "wellbutrin" for instance, records that were originally "bupropion", which is chemically equivalent are also included. A benefit of doing it this way is users don't have to find all potential names for a generic drug and drag each separately to the query panel.
As far as the ontology tree, we are using a simple alphabetic tree, and using basic brand/generic names under each. At first we had a tree that had drug classifications, but the alphabetic list seemed simpler to navigate as users seem to start with drug names in mind.
James

From: Lisa Miao [lmiao.regenstrief]
Sent: Monday, March 12, 2012 10:41 AM
To: i2b2 AUG Members
Subject: drug data
Dear all,
Has anyone successfully loaded patient drug data into i2b2? I would greatly appreciate if anyone can share some experience.
The issues that we encountered are, what drug codes should be used? I wouldn't think NDC codes are practical, since there are over 800k NDC codes, and they are continuing to develop. The i2b2demodata does have NDC codes, I suspect it's a subset, because having 800k to the term tree isn't going to be practical. Could i2b2 team comment on this?
I've tried to load RxNorm codes into the term tree. Trouble is there isn't a good tree structures for RxNorm codes. The second level (which I think are all the ingredients) have about 5000 ingredients. When I put them into i2b2, and try to expand, the webclient isn't able to expand the tree. I would assume it's because of the number of nodes.
Anyone has any experiences?
Thanks,



NEXT EMAIL
From: Chan, Wayne [Wayne.Chan.umassmed]
Sent:Monday, March 12, 2012 12:40 PM
To:Mendis, Michael E.
Cc: Donahoe, Janice M; Peter Beninato; i2b2 AUG Members
Subject:RE: Previous Query
Would you say it'll be within the next few months? Thanks.
Wayne

From: Mendis, Michael E. [MMENDIS.PARTNERS]
Sent: Monday, March 12, 2012 12:36 PM
To: Chan, Wayne
Cc: Donahoe, Janice M; Peter Beninato; i2b2 AUG Members
Subject: Re: Previous Query
WIll be part of 1.6.03
Mike

On Mar 12, 2012, at 11:50 AM, Chan, Wayne wrote: Janice,
Thanks so much for the follow up. Do you have an estimate as to when a fix will be available?
Wayne

From: Donahoe, Janice M [JDONAHOE.PARTNERS.ORG] Sent: Monday, March 12, 2012 10:48 AM
To: Chan, Wayne; Peter Beninato; members.i2b2aug<i2b2 AUG Members> Subject: RE: Previous Query
Hi Wayne,
Thanks for the email. I took a closer look at the original issue you reported and you are correct there is a problem with the web client temporarily freezing when trying to delete a previous query. The same problem exists if you try to delete a patient set or an encounter set. I have spoken to the developer and he is looking at fixing this issue.
As far as clarification on "The previous query itself cannot be edited" what I mean is the concepts, modifiers, date and value constraints that are defined when the original query was run cannot be changed. This does not include deleting the previous query from the panel in the new query or setting new constraints that are associated with the new query.
Thanks again for finding the issue with deletions.
Janice

From: Chan, Wayne [Wayne.Chan.umassmed]
Sent: Friday, March 09, 2012 4:56 PM
To: Donahoe, Janice M; Peter Beninato; i2b2 AUG Members<mailto:members.i2b2aug.org>
Subject: RE: Previous Query
Janice,
Thanks for the clarifications. So, when you said that "The previous query itself cannot be edited" (in the case of " Drag/Drop the previous query into a panel (group)"), that would include the "delete" command? If so, why would any attempt to do so result in
1) temporary (several minutes) "freeze" or "lost" of response?
2) momentary availability of the "delete" command when the webclient recovers?
as I outlined in my original email?

From: Donahoe, Janice M [JDONAHOE.PARTNERS] Sent: Friday, March 09, 2012 2:51 PM
To: Chan, Wayne; Peter Beninato; members.i2b2aug<i2b2 AUG Members> Subject: RE: Previous Query
Hi Wayne, Lisa and Peter,
There are two different functionalities happening and depending on where you drop the previous query will determine the outcome.
1. Drag/Drop the previous query to the Query name field.
Will work as a "previous query" - meaning all the items from the original query will default into the panels.
Can be edited; original items can be removed, constraints can be changed, etc.
2. Drag/Drop the previous query into a panel (group)
Will work as a "query within a query".
The previous query itself cannot be edited BUT additional items can be added to the new query.
I hope this helps explain the difference.
Janice

From: Chan, Wayne [Wayne.Chan.umassmed] Sent: Friday, March 09, 2012 1:36 PM
To: 'Peter Beninato'; members.i2b2aug<i2b2 AUG Members> Subject: RE: Previous Query
Peter,
Thanks. Your suggestion works. In fact, dropping it onto the query name would work as in previous webclient versions, i.e. even the Query Status are display (not displayed when dropping it onto a Group panel).
Another thing about dropping a prev query onto a Group panel is that the "Clear" button at the bottom can still be used to remove that pq provided that no attempt has been made to use its delete command (in fact, right-click it) first.
So, with webclient v1.6.0.2, the only viable way of re-using a pq is to drop it onto the query name field only! May be all these additional info would help pinpoint where the problem lies?!
Wayne
S. Wayne Chan, MSEE, MSME
Biomedical Research Informatics Development Group (BRIDG) and Biomedical Research Informatics Consultation & Knowledge Service (BRICKS),
Division of Health Informatics & Implementation Science (HIIS), Department of Quantitaive Health Sciences (QHS),
University of Massachusetts Medical School (UMMS) at Worcester, MA 01655 (508) 856-8947

[].edu] Sent: Friday, March 09, 2012 1:12 PM
To: Chan, Wayne; 'Lisa Miao'; members.i2b2aug.or (mailto:Miao'; members@i2b2aug.or)g<members.i2b2aug> Subject: RE: Previous Query
I see that the query name is blank.
There are two modalities. One is to drag the query and drop into the panels. The other is to drop onto the query name. I think if you drop onto query name you may have a better outcome.
From: Chan, Wayn[]] Sent: Friday, March 09, 2012 10:03 AM
To: 'Lisa Miao'; i2b2 AUG Members<i2b2 AUG Members> Subject: RE: Previous Query
Lisa,
Did any one reply to your post (attached below)???
I just encountered something very similar to what you described: On i2b2 webclient v1.6.0.2:
Once you drag the prev query over to the "Query Tool" panel, it "freezes" most usual functionalities associated with a regular concept in there (i.e. can't expand or delete, etc.). You can still "run Query" or drag over another new concept, but that concept would also become "unmanageable" (i.e. can't expand or delete, etc.).
On the other hand, if you drag over yet another concept but place it in a different "Group" (e.g. "Group 2" vs. "Group 1", where the "PrevQuery" is), then it remains "manageable" (i.e. can't expand or delete, etc.) - or not in the same group, not affected by it!
Now, sometimes if you try to right-click the "(PrevQuery)" to get at the "delete" command too many times, the entire webclient can freeze up for quite a few minutes. If & when the webclient recovers, then the "delete" command may appear very briefly (if you catches it & react in time, you might be able to actually delete it & move on, otherwise it remains "untouchable" again).
In some of the worst cases, you'll see this (at least on Chrome):
Wayne
S. Wayne Chan, MSEE, MSME
Biomedical Research Informatics Development Group (BRIDG) and Biomedical Research Informatics Consultation & Knowledge Service (BRICKS),
Division of Health Informatics & Implementation Science (HIIS), Department of Quantitaive Health Sciences (QHS),
University of Massachusetts Medical School (UMMS) at Worcester, MA 01655 (508) 856-8947

From: Lisa Miao [lmiao.regenstrief] Sent: Wednesday, February 22, 2012 9:09 AM
To: members.i2b2aug.org<members.i2b2aug> Subject: Previous Query
Hello everyone,
Is it a known bug that after you drag the previous query to run it, you won't be able to delete it, and you have to restart i2b2 to get rid of it?
Has anyone been able to get rid of the previous query once you run it? Should I file a jira ticket for this?
Thanks,
Lisa.



NEXT EMAIL
From: Russ Waitman [rwaitman.kumc]
Sent:Monday, March 12, 2012 11:21 AM
To: i2b2 AUG Members; Lisa Miao
Cc:Dan Connolly; Nathan Graham
Subject:Re: drug data

Lisa,
We loaded dispensed meds quickly out of our Epic clarity instance into our repository last year but are revisiting this issue to pull different representations of meds (admins, orders, home meds) and exploit the modifier feature of 1.6. When we get that done we should have something worth sharing.
That said, we used the internal Epic hierarchy here our i2b2 ontology. We harvest it out of the content tables in Epic and build a simple ontology, not very deep. I think it's underlying data here may be based on FDB or AHSF.
Matvey Palchuk and Recombinant did some interesting work trying to map to RxNorm and the FDA NDF-RT. I didn't here back from their customer site on whether RxNorm+NDF-RT was "good enough" or it dropped things that caused issues. I'll cut and paste his response to my prior email below:


Russ Waitman
Associate Professor, Director of Medical Informatics
Department of Biostatistics
Assistant Vice Chancellor for Enterprise Analytics
University of Kansas Medical Center
913-945-7087 rwaitman.kumc http://informatics.kumc

Matvey Palchuk <MPalchuk.recomdata> 11/10/2011 9:36 AM
We developed an RxNorm/NDF-RT hierarchy for SHRINE at Harvard Catalyst. It was subsequently refined - see citation below.
We used VA product classes - something the VA folks were not happy about. Apparently they are focusing on things like
Mechanism of Action and such for FDA structured labeling, and not maintaining the therapeutic classification.
I am not sure about AHFS - believe the sell a mapping to RxNorm. Matvey
AMIA Annu Symp Proc. 2010; vol. 2010 pp. 577-81
Enabling Hierarchical View of RxNorm with NDF-RT Drug Classes. Palchuk MB, Klumpenaar M, Jatkar T, Zottola RJ, Adams WG, Abend AH
NDF-RT is the proposed source of drug classification information. We set out to construct a hierarchy of NDF-RT drug classes and RxNorm medications and evaluate it on medication records data. NDF-RT and RxNorm are distributed in different file formats, require different tools to manipulate and linking the two into a hierarchy is a non-trivial exercise. Medication data in RxNorm from two institutions was constrained by the hierarchy. Only 37% of records from one and
65% from another institution were accessible. We subsequently enriched the RxNorm mapping in NDF-RT by exploiting relationships between concepts for branded and generic drugs. Coverage improved dramatically to 93% for both institutions. To improve usability of the resulting hierarchy, we grouped clinical drugs by corresponding clinical drug form.
PMID: 21347044
PMCID: PMC3041416
URL - http://www.ncbi.nlm.nih.gov/pubmed/21347044?dopt=Citation

On Nov 10, 2011, at 9:03 AM, "Russ Waitman" <rwaitman.kumc> wrote:
We need to revisit meds. That said, currently we use the hierarchy we pull out of the Epic meta data. I think it's based on FDB. In a future ideal state, I'd map that to RxNorm and then give people options for NDF-RT or AHFS.
Russ

Lisa Miao <lmiao.regenstrief> 3/12/2012 9:41 AM
Dear all,
Has anyone successfully loaded patient drug data into i2b2? I would greatly appreciate if anyone can share some experience.
The issues that we encountered are, what drug codes should be used? I wouldn't think NDC codes are practical, since there are over 800k NDC codes, and they are continuing to develop. The i2b2demodata does have NDC codes, I suspect it's a subset, because having 800k to the term tree isn't going to be practical. Could i2b2 team comment on this?
I've tried to load RxNorm codes into the term tree. Trouble is there isn't a good tree structures for RxNorm codes. The second level (which I think are all the ingredients) have about 5000 ingredients. When I put them into i2b2, and try to expand, the webclient isn't able to expand the tree. I would assume it's because of the number of nodes.
Anyone has any experiences?
Thanks,


NEXT EMAIL
From: Henderson, Darren W [darren.henderson.uky]
Sent:Monday, March 12, 2012 10:32 AM
To: Churchill, Susanne E.; i2b2 AUG Members
Subject:RE: San Francisco AUG Meeting
I apparently can't read. My mistake. Darren W. Henderson
Database Analyst
Center for Clinical and Translational Science Division for Biomedical Informatics University of Kentucky
789 S. Limestone Rm. 182
Lexington, KY 40536 (859) 323-7146

From: Churchill, Susanne E. [SCHURCHILL.PARTNERS] Sent: Monday, March 12, 2012 10:21 AM
To: Henderson, Darren W; i2b2 AUG Members
Subject: RE: San Francisco AUG Meeting
The entire meeting will be videotaped and made available shortly after the meeting.

From: Henderson, Darren W [darren.henderson.uky] Sent: Mon 3/12/2012 10:16 AM
To: Churchill, Susanne E.; i2b2 AUG Members
Subject: RE: San Francisco AUG Meeting
Hello all,
Could this meeting be recorded and made available online somewhere? I am really interested in hearing about all the topics listed in the agenda, but unfortunately my air travel booking has me arriving in San Francisco as the meeting is coming to a close. Thanks!

Darren W. Henderson
Database Analyst
Center for Clinical and Translational Science Division for Biomedical Informatics University of Kentucky
789 S. Limestone Rm. 182
Lexington, KY 40536 (859) 323-7146

From: Churchill, Susanne E. [SCHURCHILL.PARTNERS] Sent: Friday, March 09, 2012 2:13 PM
To: i2b2 AUG Members
Subject: San Francisco AUG Meeting
Colleagues,
Reminding those of you who will be at the Translational AMIA meetings that we have scheduled a mini-AUG meeting/workshop for Tuesday, March 20 from 6:30-8:30 in the Mission Room of the Parc 55 Hotel. This will be recorded and available on via our website shortly after the meeting. Here's the high level agenda:
1. Community Involvement - Shawn Murphy 2. 1.6 Highlights (Text Search and, on the horizon, Temporal Queries) - Shawn Murphy 3. 1.7 Preview - Shawn Murphy 4. New Ontology app - Lori Phillips 5. UCRex (5 site SHRINE network) - Lisa Dahm 6. RECEPTION
Also, we just updated our website with a new page listing "i2b2 Installations" (www.i2b2.org/work/i2b2_installations.html
<file://www.i2b2.org/work/i2b2_installations.html> ) - thanks to those of you who helped with this. Please review and let me know if there are any corrections, additions, deletions, etc. Note that this iteration does not list the CTSA Partners separately (but does call them out in the main CTSA listing).
Thanks, Susanne



NEXT EMAIL
From: Chan, Wayne [Wayne.Chan.umassmed]
Sent:Friday, March 09, 2012 7:56 PM
To:Wilson, Brian; Donahoe, Janice M; Peter Beninato; i2b2 AUG Members
Subject:RE: Previous Query

In webclient v1.3, I can d-n-d a whole pq into a group panel, and then the component concepts are immediately displayed in their respective Group panels (i.e. cc1 in gp1, cc2 in gp2, cc3 in gp3). Each of these component concepts
can be "delete"d at will (via each's "delete" command, thru right-click). In addition, the name of that pq is also displayed in the "Query Name" field – of course, when 1 cc is deleted, then the name of the pq disappears from the Query Name field.
Inccidentally, a webclient v1.3 (and I think also true up to webclient v1.6RC2) pq only consists of "patient set" & "patient count", no "encounter set".
I think it's great that webclient v1.6.0.2 pq's can now consist of "encounter set". However, the new d-n-d GUI & the new differentiation of GUI behavior (whether a pq is dropped onto the "Query Name" field or the "Group panel") can cause appreciable confusions with established i2b2 user base (i.e. the researchers that actually use it to run & reuse queries). I know I was. The GUI lock situation probably would not endear too many of our users either.

From: Wilson, Brian [BWILSON6.PARTNERS]
Sent: Friday, March 09, 2012 5:11 PM
To: Donahoe, Janice M; Chan, Wayne; Peter Beninato; i2b2 AUG Members
Subject: RE: Previous Query
Wayne & Lisa,
Do you observer the same issues - Webclient UI locking, up if you just drag the patient set from the pq rather than the whole previous query into a panel as a nested query ?
In previous version I don't believe you were allowed to drag and drop a whole pq into a panel, not sure if this is a new feature or a bug (wink) as dragging and
dropping a pq that contains both an encounter set and patient set could get confusing.
But to confirm, if I drag and drop the whole pq into the panel it locks up the UI if I try edit/modify the pq that I added, however if I leave it alone I can add other concepts and can run the query, however it does not return to
webclient (though completes successfully on the db), logging out/in the results are available.
Firefox 10.0.2

From: Donahoe, Janice M
Sent: Fri 3/9/2012 2:51 PM
To: Chan, Wayne; Peter Beninato; i2b2 AUG Members
Subject: RE: Previous Query
Hi Wayne, Lisa and Peter,
There are two different functionalities happening and depending on where you drop the previous query will determine the outcome.
1. Drag/Drop the previous query to the Query name field.
Will work as a "previous query" - meaning all the items from the original query will default into the panels.
Can be edited; original items can be removed, constraints can be changed, etc.
2. Drag/Drop the previous query into a panel (group)
Will work as a "query within a query".
The previous query itself cannot be edited BUT additional items can be added to the new query.
I hope this helps explain the difference.
Janice

From: Chan, Wayne [Wayne.Chan.umassmed] Sent: Friday, March 09, 2012 1:36 PM
To: 'Peter Beninato'; i2b2 AUG Members
Subject: RE: Previous Query
Peter,
Thanks. Your suggestion works. In fact, dropping it onto the query name would work as in previous webclient versions, i.e. even the Query Status are display (not displayed when dropping it onto a Group panel).
Another thing about dropping a prev query onto a Group panel is that the "Clear" button at the bottom can still be used to remove that pq provided that no attempt has been made to use its delete command (in fact, right-click it) first.
So, with webclient v1.6.0.2, the only viable way of re-using a pq is to drop it onto the query name field only!
May be all these additional info would help pinpoint where the problem lies?!
Wayne
S. Wayne Chan, MSEE, MSME
Biomedical Research Informatics Development Group (BRIDG) and Biomedical
Research Informatics Consultation & Knowledge Service (BRICKS),
Division of Health Informatics & Implementation Science (HIIS), Department of Quantitaive Health Sciences (QHS),
University of Massachusetts Medical School (UMMS) at Worcester, MA 01655 (508) 856-8947

From: Peter Beninato [beninato.ohsu.edu] Sent: Friday, March 09, 2012 1:12 PM
To: Chan, Wayne; 'Lisa Miao'; i2b2 AUG Members
Subject: RE: Previous Query
I see that the query name is blank.

There are two modalities. One is to drag the query and drop into the panels. The other is to drop onto the query name.
I think if you drop onto query name you may have a better outcome.

From Chan, Wayne [[Wayne.han.umassmed]|mailto:Wayne.han@umassmed.edu]
Sent: Friday, March 09, 2012 10:03 AM
To: Lisa Miao; members.i2b2aug.ord
Subject: RE: Previous Query
Lisa,
Did any one reply to your post (attached below)???
I just encountered something very similar to what you described: On i2b2 webclient v1.6.0.2:
Once you drag the prev query over to the "Query Tool" panel, it "freezes" most usual functionalities associated with a regular concept in there (i.e. can't
expand or delete, etc.). You can still "run Query" or drag over another new concept, but that concept would also become "unmanageable" (i.e. can't expand or delete, etc.).
On the other hand, if you drag over yet another concept but place it in a different "Group" (e.g. "Group 2" vs. "Group 1", where the "PrevQuery" is), then it remains "manageable" (i.e. can't expand or delete, etc.) - or not in the same group, not affected by it!
Now, sometimes if you try to right-click the "(PrevQuery)" to get at the
"delete" command too many times, the entire webclient can freeze up for quite a few minutes. If & when the webclient recovers, then the "delete" command may appear very briefly (if you catches it & react in time, you might be able to actually delete it & move on, otherwise it remains "untouchable" again).
In some of the worst cases, you'll see this (at least on Chrome):
Wayne
S. Wayne Chan, MSEE, MSME
Biomedical Research Informatics Development Group (BRIDG) and Biomedical
Research Informatics Consultation & Knowledge Service (BRICKS),
Division of Health Informatics & Implementation Science (HIIS), Department of Quantitaive Health Sciences (QHS),
University of Massachusetts Medical School (UMMS) at Worcester, MA 01655
(508) 856-8947

From: Lisa Miao [lmiao.regenstrief] Sent: Wednesday, February 22, 2012 9:09 AM[ To: i2b2 AUG Members|mailto:members@i2b2aug.org]
Subject: Previous Query
Hello everyone,
Is it a known bug that after you drag the previous query to run it, you won't be able to delete it, and you have to restart i2b2 to get rid of it?
Has anyone been able to get rid of the previous query once you run it?
Should I file a jira ticket for this?
Thanks,
Lisa.



NEXT EMAIL
From:Churchill, Susanne E.
Sent:Friday, March 09, 2012 2:13 PM
To: i2b2 AUG Members
Subject:San Francisco AUG Meeting
Colleagues,
Reminding those of you who will be at the Translational AMIA meetings that we have scheduled a mini-AUG meeting/workshop for Tuesday, March 20 from 6:30-8:30 in the Mission Room of the Parc 55 Hotel. This will be recorded and available on via our website shortly after the meeting. Here's the high level agenda:
1.) Community Involvement - Shawn Murphy
2.) 1.6 Highlights (Text Search and, on the horizon, Temporal Queries) - Shawn Murphy
3.) 1.7 Preview - Shawn Murphy
4.) New Ontology app - Lori Phillips
5.) UCRex (5 site SHRINE network) - Lisa Dahm
6.) RECEPTION
Also, we just updated our website with a new page listing "i2b2 Installations" (www.i2b2.org/work/i2b2_installations.html) - thanks to those of you who helped with this. Please review and let me know if there are any corrections, additions, deletions, etc. Note that this iteration does not list the CTSA Partners separately (but does call them out in the main
CTSA listing).
Thanks, Susanne



NEXT EMAIL
From:Mendis, Michael E.
Sent:Thursday, March 08, 2012 9:21 AM
To:Wei,Xintao
Cc: i2b2 AUG Members
Subject:Re: registered cell problem
Xintao,
When you see the managed cell, and click on it do you see a list of cells such as Ontology, CRC, ect?
mike

On Mar 5, 2012, at 1:32 PM, Wei,Xintao wrote: Hi,
I am trying to install I2B2 1.6.02 on MS server 2008. After configuring PM, I logged in the admin webpage and tried to change the IP address and port number for my cells. However, I cannot save any changes on any "Manage cells" pages or "add new cell". I can create users and save them, and I can manage projects and save changes, but not cells. Any
suggestions? Thank you,
Xintao



NEXT EMAIL
From: Natter, Marc [Marc.Natter.childrens.harvard]
Sent:Monday, March 05, 2012 8:52 PM
To: i2b2 AUG Members
Subject:Re: i2b2: data requests
Hi Tamara,
We are providing data in two forms for export for our users – one is the one fact per row format (your "long & skinny") and the other is a pivoted table based on subject ID, date, and type of event (for our registry we have different electronic data capture forms keyed to different events, e.g. baseline visit, follow-up visit, etc) as a compound index to consolidate facts into columns. We have prototyped an R based solution using Rserve from our web client (we are using Keith Marsolo's/Cincinnati Children's web client), and while it's currently not very fast for very large data sets, it only takes
about 3 lines of R code to generate the pivoted frame using the 'reshape' package for R, and then export as csv (smile) .
There is also an Excel add-in from Tableau Software that they freely distribute to reshape Excel data - http://kb.tableausoftware/articles/knowledgebase/addin-reshaping-data-excel
The add-in takes a bit of experimenting to work and is not well documented, but perhaps it could be customized in visual basic if you were looking for an alternative approach?
Will be interested to hear what ends up working for you and others.
Sincerely,
Marc
Marc Natter, MD
Intelligent Health Lab | Children's Hospital Informatics Program
Children's Hospital Boston

From: Tamara McMahon <tmcmahon.kumc<tmcmahon.kumc>> Date: Mon, 5 Mar 2012 16:12:29 -0600
To: <members.i2b2aug<members.i2b2aug>>
Subject: i2b2: data requests
Hello,
I am curious as to how members of this community send data when requested. My institution has received numerous requests lately for data, and we are in the process of determining how to fulfill these requests. Currently we provide data in the entity-attribute-value model (aka "long & skinny") but users do not know what to do with it.
Does your institution fulfill data requests? If so, do you transform the data into a more columns-oriented model? Do you use any tools for these transformations?
I am currently reviewing the ExportXLS plugin but am also looking for other methods people use. I appreciate any feedback.
Regards,
Tamara McMahon
Clinical Informatics Coordinator Department of Biostatistics University of Kansas Medical Center
913-945-7470
http:1/informatics.kumc.edu/



NEXT EMAIL
From: Henderson, Darren W [darren.henderson.uky]
Sent:Monday, March 05, 2012 10:48 AM
To: Pablo, Ray; i2b2 AUG Members
Subject:RE: Hide Patient Set Checkbox from obfuscated users

You may still wish to offer the Patient Set result as a feature since it can also be dragged back into the Query UI to further refine, or use as a concept in some way exclusion or inclusion criteria. An obfuscated user can neither expand nor see an exact count when a patient set is produced for them and stored in the Previous Queries area of the UI. If you do wish to completely remove the result type, you can set its visual attribute to LH in the QT_QUERY_RESULT_TYPE table.
My answer above reflects how Patient Sets behave in 1.6.02.

From: Pablo, Ray [pablorp.uci.edu]
Sent: Friday, March 02, 2012 3:49 PM
To: i2b2 AUG Members
Subject: Hide Patient Set Checkbox from obfuscated users
We are on i2b2 web client v.1.5.4
How can we hide the patient set checkbox option for obfuscated users when they run queries? Since they won't have the permission to view patient sets or run any analysis tools, we don't think this should be visible to them.
Thanks
Ray Pablo | Business Intelligence Developer | University of California, Irvine | 200 S. Manchester Avenue, Suite 508 | Orange, CA
92868 | ?: 714.456.6374 | ?: pablorp.uci



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From: Heilala, Christopher P [HEILALA.CHRISTOPHER.mcrf.mfldclin\] (mailto:.CHRISTOPHER@mcrf.mfldclin.edu)
Sent:Friday, March 02, 2012 3:53 PM
To: Pablo, Ray; i2b2 AUG Members
Subject:RE: Hide Patient Set Checkbox from obfuscated users
Hey Ray,
What we did for this was to modify the default.htm code in the Web Client Folder:
The code to be removed is found in the default.htm page within the 'webclient' folder on the server (D:\Opt\Apache
Software Foundation\Apache2.2\htdocs\webclient), or where ever you installed the Apache Server:
<div id="crcDlgResultOutputPRS"><input type="checkbox" class="chkQueryType" name="queryType" value="PRS" /> Patient Set (list of matching patients)</div>
This code is found on line 815, within the 'Query Run Dialog' section.
I simply commented out this bit of code in the event that we ever needed it again. Keep in mind that by removing this code, no one will be able to see the patient sets from the Web Client side of things. There may be a better option for removing this for particular users.
Chris

From: Pablo, Ray [pablorp.uci.edu]
Sent: Friday, March 02, 2012 2:49 PM
To: i2b2 AUG Members
Subject: Hide Patient Set Checkbox from obfuscated users
We are on i2b2 web client v.1.5.4
How can we hide the patient set checkbox option for obfuscated users when they run queries? Since they won't have the permission to view patient sets or run any analysis tools, we don't think this should be visible to them.
Thanks
Ray Pablo | Business Intelligence Developer | University of California, Irvine | 200 S. Manchester Avenue, Suite 508 | Orange, CA
92868 | ?: 714.456.6374 | ?: pablorp.uci



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From: Pablo, Ray [pablorp.uci]
Sent:Friday, March 02, 2012 12:36 PM
To:Chan, Wayne; 'i2b2 AUG Members'
Subject:RE: Caveat alert concerning the ExportXLS web client plugin from UMass Med School & Universita' di Pavia
Attachments:image001.png; image002.png

Hi Wayne,
Thank you for developing this webclient plug?in. I have a question regarding browser compatibility. We've been experiencing some hang ups running the plug?in from IE v8.0 but they would run successful in Chrome. The performance in Chrome appears to be pretty quick with a patient set of nearly 5,000. Could this still be a bug reported in v2?
Thanks, Ray

From: Chan, Wayne [Wayne.Chan.umassmed]
Sent: Monday, February 27, 2012 9:29 AM
To: 'i2b2 AUG Members'
Cc: 'Mauro Bucalo'; Sadasivam, Rajani; Houston, Thomas
Subject: Caveat alert concerning the ExportXLS web client plugin from UMass Med School & Universita' di Pavia
Hi, All,
Our special thanks to Gregory Schulte (Children's Hospital Colorado), who has alerted us that if the "short_open_tag" in the php.ini file of a server (of this web client plugin) is NOT set to* "on*", then the resulting exported Excel spreadsheet may be just a blank file.
He also suggested the following alternatives as workaround options (for those who have encountered this "blank file" problem, else one need not do anything):
either change the "short_open_tag" in the php.ini file to short_open_tag = On
or change line 15 of the SaveToExcel.php file, from
<body><?=$_REQUEST['datatodisplay']?>
to
<body><?php echo $_REQUEST['datatodisplay']?>

Of these, we recommend updating the php.ini file.
Incidentally, we determined that this caveat exists for v1.0-2.0 of this web client plugin.
We do hope to have an updated SaveToExcel.php file (that takes care of this caveat without requiring the deployers to update their php.ini files) included in the next release of this web client plugin.
BTW, we have also added this info to the new "Caveats" page of the ExportXLS i2b2 Community wiki (https://community.i2b2.org/wiki/display/ExportXLS/Caveats), as well as updated the corresponding "Features Requested" page with this, for future references.
Thanks.

From: Chan, Wayne
Sent: Friday, February 24, 2012 10:01 AM
To: 'i2b2 AUG Members'
Cc: Sadasivam, Rajani; Houston, Thomas; 'Mauro Bucalo'; Zottola, Ralph; Ranauro, Paul; English, Thomas
Subject: i2b2 community wiki project page for ExportXLS web client plugin from UMass Med School & Universita' di Pavia
Hi, All,
Per Shawn's invitation, and thanks to Mike's helps, we now have the ExportXLS wiki page set up on the i2b2 Community Dashboard (https://community.i2b2.org/wiki/display/ExportXLS/ExportXLS+Home):
Alternatively, you can also get there by clicking on the ExportXLS link on the i2b2 Community Dashboard
(https://community.i2b2.org/wiki/dashboard.action) itself:
Thanks.

From: Mike Mendis [mmendis.partners]
Sent: Thursday, February 23, 2012 3:24 PM
To: Chan, Wayne
Subject: Re: ExportXLS v2.0 plugin (for webclient) from UMass Med School & Universita' di Pavia
All set

From: Chan, Wayne
Sent: Wednesday, February 22, 2012 10:17 AM
To: Murphy, Shawn N.; Mendis, Michael E.
Subject: RE: ExportXLS v2.0 plugin (for webclient) from UMass Med School & Universita' di Pavia
Shawn & Mike,
Thanks, sure, it'll be our pleasure to do that. Please send me the URL and instructions.
Wayne
S. Wayne Chan, MSEE, MSME
Biomedical Research Informatics Development Group (BRIDG) and Biomedical Research Informatics Consultation & Knowledge Service (BRICKS), Division of Health Informatics & Implementation Science (HIIS),
Department of Quantitaive Health Sciences (QHS),
University of Massachusetts Medical School (UMMS) at Worcester, MA 01655 (508) 856?8947

From: Murphy, Shawn N. [SNMURPHY.PARTNERS]
Sent: Tuesday, February 21, 2012 5:44 PM
To: Chan, Wayne
Cc: i2b2 AUG Members; Sadasivam, Rajani; Houston, Thomas; Mauro Bucalo; Zottola, Ralph; Ranauro, Paul; English, Thomas;
Kinney, Rebecca; Phillips, Barrett D
Subject: Re: ExportXLS v2.0 plugin (for webclient) from UMass Med School & Universita' di Pavia
Hi Wayne and team,
This is a great resource for our community, and would very much like to have this put up on the community web site. Mike and our team can facilitate this with your own space if you would like.
Thanks,
Shawn Murphy MD Communicating with handheld

On Feb 21, 2012, at 1:35 PM, "Chan, Wayne" <Wayne.Chan.umassmed> wrote:
Hi, all,
As a collaborative effort, we at University of Massachusetts Medical School and Universita' di Pavia are very happy to announce that the v2.0 of the ExportXLS plugin (for webclient). This release is compatible with i2b2 v.1.3-1.6, as well as compatible with the 4 major web browsers (Firefox, Internet Explorer, Chrome, & safari). New Features in this Release (v2.0)
Based on feedbacks and input from other researchers, we have made the following updates, adjustments, enhancements, and fixes that may better serve everyone in the i2b2 community:
1.) Updated patient_list params to render this plugin compatible with i2b2 v1.3; and fixed a problem in the version for i2b2 v1.6 (it should now work on i2b2 v1.3?
v1.6).
2.) Added table title and caption to the resulting output table.
3.) Added new 1st column for patient row counts (no column title).
4.) Renamed the "StateCity" column title to "State/City".
5.) Removed any leading and trailing redundant "Zip codes" values from each state value string.
6.) Defaulted to using "concept_cd" for each selected concept entry if neither "tval_char" nor "nval_num" is available.
7.) Improved efficiencies.
8.) Facilitated the flexible dropping of any columns (that may contain data too sensitive or personal) from the resulting output table.
9.) Fixed the Internet Explorer (IE) hang problem.
10.) Fixed the missing "concept" columns on IE problem.
11.) Fixed the blank "patient_IDs" (when "Include Patient Date" not selected) on IE problem.
12.) Fixed table content getting cutoff on IE problem.
13.) Centered content in each table cell of the resulting output table.
14.) Added unique time?stamp to name of exported XLS file.
15.) Updated the description of this plugin displayed (in the available plugin list), to<image003.jpg>
16.) Added more descriptions in the "Specify Data" and "Plugin Help" tab pages.
17.) Updated plugin category from "text" to "standard".
This new release is packed with installation guide and version supplementary note, and is available now from Google Codes (http://code.google/p/i2b2?export?xls?plugin/downloads/detail?name=ExportXLS?v2.0?20120217.zip&can=2&q=#makechanges). It will also be available from the UMass Med School MICARD Downloads page (http://micard.umassmed.edu/downloads.php) by next Tuesday, 2/28.
Please don't hesitate to contact us concerning any questions or problems. Thanks.



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From:Murphy, Shawn N.
Sent:Thursday, March 01, 2012 11:18 AM
To: Yves Thorrez; i2b2 AUG Members
Subject:RE: Cancelling a query
Hi Yves,
Yes, the cancel button is purely to free up the User Interface. The actual query continues to run until the designated timeout (usually 3 minutes). The other effect of the cancel is to prevent it from being placed in the next queue with a longer timeout.
Thanks, Shawn.

From: Yves Thorrez [Yves.Thorrez.uzbrussel.be]
Sent: Thursday, March 01, 2012 9:03 AM
To: 'i2b2 AUG Members'
Subject: Cancelling a query
Hi,
We have i2b2 v1.6.02 on SQL Server 2008. When a query is cancelled through the web client, it is still running to completion in SQL Server, consuming considerable server resources.
Anyone else experiencing this? Thanks,
Yves



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From:Mendis, Michael E.
Sent:Thursday, March 01, 2012 9:47 AM
To:Yves Thorrez
Cc: i2b2 AUG Members
Subject:Re: Cancelling a query

When you cancel a query it will complete in the current queue that is it in, but will not progress to the next queue if it needs to.So when you cancel a query it stop it from going to the next queue, but does not atop it from currently running.
mike

On Mar 1, 2012, at 9:02 AM, Yves Thorrez wrote:
Hi,
We have i2b2 v1.6.02 on SQL Server 2008. When a query is cancelled through the web client, it is still running to completion in SQL Server, consuming considerable server resources.
Anyone else experiencing this?
Thanks,
Yves