i2b2 Academic Users Group
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Last Updated: 09/30/2011



NEXT EMAIL
From: Brian Ostasiewski [bostasie.wakehealth] Sent: Friday, September 30, 2011 2:28 PM To: Travis Nagler; i2b2 AUG Members Subject: RE: Change title on i2b2 login screen
js-i2b2/cells/PM/PM_misc.js: ' <div class="hd">i2b2 Login</div>\n'+
I'd give you a line number but we've already modified ours from the distributed version.

From: Travis Nagler [travis.nagler.ucdmc.ucdavis] Sent: Friday, September 30, 2011 2:21 PM To: i2b2 AUG Members Subject: Change title on i2b2 login screen
We are running 1.5.2. We're to the point of doing some minor tweaks, one of which being changing the login pop-up box title to something other than "i2b2 Login".
As near as I can tell, the pop-up is called on the web default.htm page with "i2b2.PM.doLoginDialog();". Does anyone know where this function is maintained so I can make that change? We're using the default everything located in our /opt folder at this point, so if you could point out a complete file address, it would be most appreciated.
Thank ,
Travis
Travis H. Nagler
Senior Database Programmer
American Burn Assoc. - Data Coordinating Center
UC Davis Division of Burn Surgery
UC Davis Health System
2921 Stockton Blvd., Suite 1470
Sacramento, CA, 95817 http://www.ucdmc.ucdavis
travis.nagler.ucdmc.ucdavis


NEXT EMAIL
From: Peter Beninato [beninato.ohsu] Sent: Friday, September 30, 2011 1:32 PM To: Brian Ostasiewski; i2b2 AUG Members Subject: RE: i2b2 - v1.4 - Demographics Plugin - Age in Years - ISSUE
Thanks Brian.
Ok, so clearly I have issues reading some code...
I also... SEE DEAD PEOPLE (reference 6th sense).
What value would you set age_in_years_num for dead people?
Clearly, -1 may not be the best choice I made, I think my logic was something like
I may know they are dead
I may not know their death date.
Age is generally a positive number
Performance problem if left null (I think there was some sort of performance issue with nulls, so I needed a value.)
I'll set the value to <drum roll> -1
Can anyone help me modify the code so -1 isn't included in the 0-10 bucket?
Peter

From: Brian Ostasiewski [bostasie.wakehealth] Sent: Friday, September 30, 2011 10:12 AM To: Peter Beninato; i2b2 AUG Members Subject: RE: i2b2 - v1.4 - Demographics Plugin - Age in Years - ISSUE
Looking at the code for the Dem1Set plugin, if age_in_years_num is negative, it is defaulted to zero, which is then put in the zero-to-10 bucket.
What is the value being returned for age_in_years_num in the XML? It could be your 1921 example is interpreted as 2021, which would result in a negative age when subtracted from today.
Brian Ostasiewski

From: Peter Beninato [beninato.ohsu] Sent: Friday, September 30, 2011 12:44 PM To: Peter Beninato; i2b2 AUG Members Subject: RE: i2b2 - v1.4 - Demographics Plugin - Age in Years - ISSUE
Hi, Hmmm. So I developed query below to pull patient_num for an i2b2 query from the qt_master_query.query_master_id.
I grabbed the patient_list and examined patient_dimension birth_date.
The max is 09/22/1921 – MM/DD/YYYY (HIPAA 90 y/o at time of ETL run). The min is 06/5/1952.
So still confused why anyone is in the 0-10 age bucket in the Demographic plugin.
Anyway, I include the SQL for the query to get the patient list out of the data schema to share.
/*
NAME: query_for_i2b2_pat_ids_from_i2b2_patient_set_query.sql
AUTHOR: Peter Beninato
DATE: 29-Sept-2011
Purpose: To get the list of pat_ids from an
i2b2 query. *
Ususge: *
2) Query the qt_query_master table for the
query_master_id of interest.
3) Edit the SELECT of query_master_id table in the WITH
clause for the query_master_id number
4) Run query
5) Export pat_id list or plug it into another query. * *
***********************************************************************
Change the query_master_id for the particular query
This ID is found in the octrii2b2data.qt_query_master table * *********************************************************************** */
with query_master_id as (
CHANGE THE NUMBER BELOW FOR THE ID!!!!!
select <replace with master_query_id> as query_master_id
from dual
),
query_id as
(
select query_master_id.query_master_id, q_inst.query_instance_id
from query_master_id
join octrii2b2data.qt_query_instance q_inst
on query_master_id.query_master_id = q_inst.query_master_id
where status_type_id = 6
) select qry_reslt.query_master_id
,qry_reslt.query_instance_id
,qry_reslt.result_instance_id
,i2b2_pat_set.patient_num
from
(
select query_id.query_master_id
,query_id.query_instance_id
,qry_reslt_inst.result_instance_id
from query_id
join octrii2b2data.qt_query_result_instance qry_reslt_inst
on query_id.query_instance_id = qry_reslt_inst.query_instance_id
and result_type_id = 1
) qry_reslt
join octrii2b2data.qt_patient_set_collection i2b2_pat_set
on qry_reslt.result_instance_id = i2b2_pat_set.result_instance_id

From: Peter Beninato Sent: Thursday, September 29, 2011 9:35 AM To: i2b2 AUG Members Subject: i2b2 - v1.4 - Demographics Plugin - Age in Years - ISSUE
Hi,
I think we stumbled on an issue with the Demographics (1 Patient Set) - Simple Counts plugin.
The query was something like: Patient Age >= 60
DX: hypertensive ( 2 years ago).
MEDS: who are prescribed some drugs in the following year ( 1 year ago).
I2b2 returns a patient set. What was very curious is that when the patient set is viewed via the plugin...
THERE ARE PATIENTS in the 0-10 bucket!
It seems to me the logic in the snippet below may not be correct.
In our patient dimension no AGE_IN_YEARS_NUM is greater than 90 per HIPAA. Also, I peg the birth_date to no greater than 90 years ago.
In our data set we had dead people, but I can't see how a birth_date in the year 1921 ( 90 years ago when ETL was run), could put someone in the 0-10 bucket.
If this PLUGIN code is the same in v1.6 it probably needs to be reviewed.
Also, since there already is an age_in_years_num in the patient dimension why not just use that? (Or could someone maybe help me figure out how to implement that?)
I see the parsing of "T" which makes me think that some of this code might be particular to Microsoft, which sometimes pegs a date to 01/01/1900.
Anyway not sure of the solution. But I hope someone else can run a patient set through the plugin, confirm the issue, so that some work can be done to correct.
Thanks.
// get all the patient records var pData = i2b2.h.XPath(results.refXML,
'descendant::patient/param[.name]/text()/..');
var hData = new Hash();
for (var i1=0; i1<pData.length; i1++) {
var n = pData[i1].getAttribute('name');
var t1 = hData.get(thumbs down) ;
if (!t1) { t1 = new Hash(); }
var v = pData[i1].firstChild.nodeValue;
if (n=="birth_date") {
v = v.substring(0, v.indexOf("T"));
}
if (n=="age_in_years_num") {
v = Math.floor(v/10);
if (v<0) {v=0;}
if (v>9) {v=9;}
if (v==0) {v='0-10';} else {v=v+'0-'(v+1)'0';}
}
var t2 = t1.get(v);
if (!t2) { t2 = 1; } else {
t2++; } t1.set(v, t2); hData.set(n, t1);
}
Peter Beninato - OCTRI DW Developer Oregon Health & Science University
beninato.ohsu


NEXT EMAIL
From: Murphy, Shawn N. Sent: Thursday, September 29, 2011 9:02 AM To: Mauro; Michael Horvath Cc: i2b2 AUG Members Subject: RE: Current roadmap
Hi Mauro,
We are targeting the 1.6 release for next Friday pending any unforeseen issues.
Thanks, Shawn.

From: Mauro [mauro.bucalo.gmail] Sent: Thursday, September 29, 2011 5:17 AM To: Michael Horvath Cc: i2b2 AUG Members Subject: Re: Current roadmap
Any news about the final 1.6 release?
Thanks.

2011/9/15 Michael Horvath <mhorvath.wakehealth>
Is there a new estimate on when the final release will be available?

From: Murphy, Shawn N. [SNMURPHY.PARTNERS] Sent: Friday, August 12, 2011 3:11 PM To: Michael.C.Ford.kp; i2b2 AUG Members Subject: RE: Current roadmap
Hi Michael,
We are hoping to release it in early September. The plan for version 1.7 is on the front page of the i2b2 site towards the bottom.
Thanks, Shawn.

From: Michael.C.Ford.kp [Michael.C.Ford.kp] Sent: Friday, August 12, 2011 2:07 PM To: i2b2 AUG Members Subject: Re: Current roadmap
Anyone ?

From: Michael.C.Ford.kp [Michael.C.Ford.kp] Sent: Friday, August 11, 2011 8:51 AM To: i2b2 AUG Members Subject: Re: Current roadmap
Looking for the road map of the product and I can't seem to find it. I was wondering when 1.6 would become GA vs the current 1.5.4


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From: Yves Thorrez [Yves.Thorrez.uzbrussel.be] Sent: Friday, September 23, 2011 3:09 AM To: i2b2 AUG Members Subject: metadataxml: flags and reference values
Hi,
In the context of reference values for our lab results, in C_METADATAXML there are following elements:
<Flagstouse></Flagstouse>
<LowofLowValue></LowofLowValue> <HighofLowValue></HighofLowValue> <LowofHighValue></LowofHighValue> <HighofHighValue></HighofHighValue> <LowofToxicValue></LowofToxicValue> <HighofToxicValue></HighofToxicValue> 1)
The documentation states the acceptable values for 'flagstouse' as 'L' (low), 'N' (normal), 'H' (high), 'A' (abnormal) and 'X' (toxic). Is it possible to define additional flags and how they are displayed in the i2b2 client? The Demo data contains codes A, P, X, L, M in OBSERVATION_FACT::VALUEFLAG_CD
How are the remaining elements <Lowof...> and <Highof...> used when values are filled in? If we set the valueflag_cd at load time, can these elements play an additional role?
Thanks,
Yves
Yves Thorrez
Medische Informatieverwerking
yves.thorrez.uzbrussel.be
Laarbeeklaan 101 - 1090 Brussel
www.uzbrussel.be


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From: Michael.C.Ford.kp Sent: Monday, September 19, 2011 2:13 PM To: i2b2 AUG Members Subject: Eclipse Deployment
Good morning
I was wondering if anyone had a complete Eclipse based I2B2 build and deployment setup that was documented ?
Thanks in advance Michael C Ford Application Development Project Manager Division of Research 2000 Broadway Oakland Ca 041W09


NEXT EMAIL
From: Michael.C.Ford.kp Sent: Monday, September 19, 2011 1:40 PM To: i2b2 AUG Members Subject: Illegal characters in the concept dimension path
We are finding some problems with some special characters in the concept dimension path. ~ being one of these characters. I expect it's all the characters not allowed in the URL ~ # ? / \ % :
anyone know the rules on this ?


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From: Walter Knesel [Walter.Knesel.cchmc] Sent: Thursday, September 15, 2011 5:00 PM To: i2b2 AUG Members Subject: PM 1.6 RC4 miscellaneous table
Hi,
I am looking at the 1.6 RC4 PM_Design_1-6 document and I see that it mentions a PM_CODE_LOOKUP table. So I wanted to see what data was in it, etc. When I go to the RC download page, I can only find an RC5 i2b2demodata zip file. That zip file in the PM folder does not create that table or load that data.
So is this table still a future item or just missing?
Thanks, Walter Knesel


NEXT EMAIL
From: Chan, Wayne [Wayne.Chan.umassmed] Sent: Friday, September 09, 2011 9:43 AM To: I2B2 AUG Members Subject: FW: i2b2 - v1.4 - Edit login Form - Where?
That file is in <webclient>/js-i2b2/cells/PM (where <webclient> is, for instance, on my v1.3 install, it'll be /var/www/html/webclient)
Also the background picture for that login dialog is <webclient>/js-i2b2/cells/PM/assets/login_bg.jpg – one can replace that with another with the same name if so desired.
Wayne
Wayne Chan
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

From: Peter Beninato [beninato.ohsu] Sent: Thursday, September 08, 2011 6:48 PM To: Rasmussen, Luke V; I2B2 AUG Members Subject: RE: i2b2 - v1.4 - Edit login Form - Where?
Applause!
Thanks.

From: Rasmussen, Luke V [rasmussen.luke.mcrf.mfldclin] Sent: Thursday, September 08, 2011 3:22 PM To: Peter Beninato; I2B2 AUG Members
Subject: RE: i2b2 - v1.4 - Edit login Form - Where?
I'm looking at 1.5 code, but I believe you just need to go to the webclient code and modify PM_misc.js.
Luke Rasmussen Senior Programmer/Analyst Marshfield Clinic Research Foundation Biomedical Informatics Research Center

From: Peter Beninato [beninato.ohsu] Sent: Thursday, September 08, 2011 5:16 PM To: I2B2 AUG Members Subject: i2b2 - v1.4 - Edit login Form - Where?
Hi,
Where can one go and edit the title bar on the login form?
I want to edit the "i2b2 Login".
This is v1.4, I'm not compiling and deploying the application via Eclipse. Using the webclient, and would like to edit the title of the login box. But, I seem to lose the trail in PM_view.js (i2b2.PM.doLoginDialog).
Does this web form exist in the "source" so could edit it (somewhere) and redeploy via ant target?
Thanks.
Peter Beninato - OCTRI DW Developer
Oregon Health & Science University
beninato.ohsu


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From: Murphy, Shawn N. Sent: Thursday, September 08, 2011 3:53 PM To: Davis, Michael (Oncology); I2B2 AUG Members Subject: RE: 1.6 new feature - temporal constraint
Hi Mike,
Yes, that is right, a query done with the "same financial encounter" timing constraint will insist that all the elements in the query happened in the same encounter (encounter_num for techies). This constraint can be overridden in each panel though, so that if you have "male" for example that does not need to be recorded in the same encounter but you want to use it in the query, you can do that too.
Thanks, Shawn.

From: Davis, Michael (Oncology) [davismk.upmc] Sent: Thursday, September 08, 2011 2:59 PM To: Murphy, Shawn N.; I2B2 AUG Members Subject: RE: 1.6 new feature - temporal constraint
Shawn,
Good question! J I'm looking at the workbench and really referring to the Query Timing (labeled as Temporal Constraints in web client) options (i.e, Selected groups occur in the same financial encounter, etc). I'm not sure how these are working on the data. Does this option use the ENCOUNTER_NUM for grouping 'liked' transactions? Not sure.
Thanks

From: Murphy, Shawn N. [SNMURPHY.PARTNERS] Sent: Thursday, September 08, 2011 1:56 PM To: Davis, Michael (Oncology); I2B2 AUG Members Subject: RE: 1.6 new feature - temporal constraint
Hi Mike,
Which temporal constraints are you referring to, the ones controlled by SQL in the patient and visit metadata tables?
Thanks,
Shawn.

From: Davis, Michael (Oncology) [davismk.upmc] Sent: Thursday, September 08, 2011 1:50 PM To: I2B2 AUG Members Subject: RE: 1.6 new feature - temporal constraint
Is there a document that explains the usage of the Temporal Constraints features which appears on the query tool? I'm trying to figure out what this means in terms of how the fact and dimension data should be loaded to take advantage of these features.
Mike

From: Murphy, Shawn N. [SNMURPHY.PARTNERS] Sent: Saturday, July 30, 2011 8:49 PM To: I2B2 AUG Members Subject: 1.6 RC4 is Available
Please see at: https://www.i2b2.org/RC/
Thanks, Shawn.


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From: Michael.C.Ford.kp Sent: Tuesday, September 06, 2011 6:00 PM Cc: I2B2 AUG Members Subject: RE: install of the Workbench client
Thanks this issue seems to be associated with the current 1.5 release. once I installed a 1.4 release it worked fine.

From: Phillips, Lori C. Sent: 09/06/2011 11:19 AM To: Michael C Ford, I2B2 AUG Members Subject RE: install of the Workbench client
try
JAVA_HOME = C:\Program Files\Java\jdk1.6.0_16\bin
Also your classpath looks suspect I am guessing that C:\Program Files\Java\jre6\lib\ext\QTJava.zip does not exist.
perhaps try
CLASSPATH = .;C:\Program Files\Java\jdk1.6.0_16\bin

From: Michael.C.Ford.kp [Michael.C.Ford.kp] Sent: Tuesday, September 06, 2011 1:52 PM To: I2B2 AUG Members Subject: install of the Workbench client
Hello I am hoping someone can give me a pointer on install of the workbench client.
I followed the install document, but I think it's a bit light. I unpacked the windows zip file into a folder C:\i2b2Client so I have C:\i2b2Client\Windows.
Modified the I2b2Workbench.ini ( I have XP, 3 gigs 2.66GHZ )

-vmargs s -Dorg.osgi.framework.bootdelegation=* -Djava.endorsed.dirs=endorsed_lib -Xms40m -Xmx2048m


Tried to start and receive an error "Failed to create Java Virtual Machine" I have defined under system variables JAVA_HOME = C:\Program Files\Java\jdk1.6.0_16 my CLASSPATH = .;C:\Program Files\Java\jre6\lib\ext\QTJava.zip
I have eclipse Helios in a directory c:/eclipse but it's not needed.


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From: Rauscher, Richard [rrauscher.hmc.psu] Sent: Tuesday, September 06, 2011 2:26 PM To: I2B2 AUG Members Subject: position open for I2B2/clinical research data warehouse person at Penn State
Dear I2B2 Members:
We have a position open in Hershey, PA forsomeone with I2B2 administration expertise.Please see below

Data Warehousing Specialist
Location: Hershey, Pennsylvania, United States
Job Contact Name:
Richard Rauscher
Job Contact Email:
rrauscher.hmc.psu
Organization:
Penn State University
Job Description:
Penn State is seeking a data warehousing specialist to help support our clinical research enterprise.
Specifically, this individual will:
Assist clinical investigators with data requests
If necessary, act as an "honest broker" between the clinical data and requester
Ensure compliant conveyance of data
Assist in leading a project to implement the I2B2 cohort discovery tool
The ideal individual will have experience with data warehousing, a commercial Electronic Medical Record system and coding systems for medicine (such as ICD9, CPT4, SNOMED, LOINC). The extraordinary candidate will have experience with implementing I2B2 in an academic health center. Please see the official position description below.
JOB SUMMARY:
Provide technology support to one or more operational business units of the Medical Center. Participate in team planning and discussions, prepare sections of team documents, lead small to medium-sized projects, and participate in larger projects. Realize that the daily emphasis of this position is task completion and project completion, according to specific instructions. Understand that these activities usually require the implementation of known approaches, perhaps with modest modification, rather than the engineering of new solutions.
JOB REQUIREMENTS:
Either: (a) Bachelor's degree plus two additional years of related experience or (b) six years total of related experience.
PREFERRED QUALIFICATIONS:
Expertise with clinical terminology, database structure, data warehousing and data mining. Should have exposure to back-end EMR databases and familiarity with SQL and a business intelligence tool
(e.g. Business Objects). Familiarity with clinical research-related ontologies.
Penn State is committed to affirmative action, equal opportunity and the diversity of its workforce. EOE-AA-M/F/D/V
You may apply by going to https://www.healthcaresource.com/hershey/index.cfm?
fuseaction=search.jobDetails&template=dsp_job_details.cfm&cJobId=101872 external link
If you have any questions, please contact Richard Rauscher (rrauscher.hmc.psu).
Thank you.


NEXT EMAIL
From: Wilson, Brian Sent: Sunday, September 04, 2011 6:04 PM To: Viangteeravat, Dr Tee Cc: I2B2 AUG Members Subject: RE: Need Help for i2b2 webclient setup
Tee
One of the things most new users miss is compiling their apache install with curl enabled:
curl: http://en.wikipedia.org/wiki/CURL <http://en.wikipedia.org/wiki/CURL> http://www.php.net/manual/en/install.unix.apache2.php <http://www.php.net/manual/en/install.unix.apache2.php> http://www.php.net/manual/en/book.curl.php <http://www.php.net/manual/en/book.curl.php>
Might be worth checking B

From: Viangteeravat, Dr Tee [tviangte.uthsc] Sent: Sun 9/4/2011 12:00 PM To: I2B2 AUG Members Subject: Need Help for i2b2 webclient setup
I have downloaded and installed i2b2 Webclient from i2b2 source. However I got "Your account does not have access to any i2b2 projects" message when I tried to login. Did I miss anything? Please guide me what else do I need to install and configure?
Thanks so much! Tee


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From: Chanumolu, Vijayalakshmi [vijayalakshmi.chanumolu.uky] Sent: Thursday, September 01, 2011 3:51 PM To: q.t.zeng.utah; I2B2 AUG Members Subject: NLP-CELL
HI ALL,
I am trying to install the demo version of NLP.That is placing the plug-in edu.harvard.i2b2.eclipse.plugins.nlp_1.0.0.jar file in workbench 1.5.4 .
When I install the plug in in that way I thought that the client is going to connect the sever at harvard .
I am getting an error like class files are not found.I got only the 1.0 version of nlp plug in from the i2b2 website.But I get the src for the 1.5.4 version.
I have some couple of doubts:
where can I get the jar files for the current version??
Does anybody installed NLP-cell and configured it ??
I am working on it till the past two months but did not come to any conclusion.Can anybody please help me regarding this issue??
Thanks, Vijaya

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