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Last Updated: 03/18/2013



Open Source Standard Medication Ontology [06-28-2012]
From: Marsolo, Keith Sent: Thursday, June 28, 2012 2:21 PM To: Russ Waitman Cc: Andrew J. McMurry; i2b2 AUG Members; Dan Connolly; Nathan Graham Subject: Re: Is there an open source "standard" medication ontology that is being used for SHRINE and is it the i2b2 demo ontology?
Russ,
Just a head's up - you may want to require password protection for any ETL scripts you have that reference Clarity.  We had some scripts up on our public SVN and received a takedown notice from Epic's legal department.  This was after Epic gave us permission.  The only rationale we got was that Epic "changed their mind."  We suspect it's related to the upcoming release of the Epic Data Warehouse product.
So just a word of caution to you (and any other Epic customer) who has stuff publicly accessible.  In Epic's mind, sharing with customers is okay.  Sharing openly with the world is a no-no.   
Keith

On Jun 28, 2012, at 1:37 PM, Russ Waitman wrote:
Hi Andrew,
Thanks for the prompt reply.  We are aware of that article and contacted Matvey who informed us that the resulting ontologies were not freely available.
We will have it covered from getting Epic meds mapped to GCNSEQNO or NDC and then getting to RxNorm CUIs.  We're tracking our work on this topic in our ticket here http://informatics.kumc.edu/work/ticket/1048 and your free to use our stuff when its done.
What we want is once we're there, which ontology should we use for Meds that uses those CUI codes?   
Is it possible to get a copy of that ontology from you, NCBO, someone else in i2b2 compatible format (aka insert into CONCEPT_DIMENSION)?
Our sense is we would want to have our folders line up to be really cross institutional compatible.  Otherwise, you have to build your queries down at the concept code level instead of leveraging higher level paths.  We can recreate things ourself now that NDF-RT is in the UMLS with RxNorm but even then, I doubt we'd get things to line up exactly right with what you have done.  
1.  Is the i2b2 demo data "Medications" based on that standard ontology or something else?  
That demo data seems to be mapped down at the NDC level and not using RxNorm CUIs.  
I would think the NDC would be too low a level and that most researchers would want to operate a level up in the RxNorm hierarchy.  Ideally pill size should be handled in a dose modifier so you don't have to join all the pill sizes together.  
2.  Secondarily, does the keeper of the ontology have update scripts somewhere that run against RxNorm and NDF-RT that handle the weekly or monthly updates as new NDCs and drugs come on market?  Or, a way to just pickup the new concept_dimensions in a zip file or something?
Russ
McMurry, Andrew J. 6/28/2012 12:01 PM We have mapped several Medication lists to RxNorm at the Harvard hospitals.
From there, we used the National Drug File medication tree created by the VA (called NDF-RT).
This paper provides a useful description http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041416
I will check if this process has been done for EPIC specifically. 
Zak just suggested to me that we try this for EPIC if we have not done so already. 
Cheers,
andy 

On Jun 28, 2012, at 9:55 AM, Russ Waitman wrote:
Hi,
We are now re-doing our Medications so that in addition to tagging our medication observations with the local terminology (Epic medication_id), we are going to map things to RxNorm. 
 
We're motivated to do this because the local Epic ontology we harvest from Clarity is leaving a fair number of observations unmapped and also because we want to enter this world of interoperability. 
 
Our approach to mapping is if we get hit on GCNSEQNO  we use it, elseif we have NDC we use it.  Our fallback in then going to be using MedEX for an NLP lookup to RxNorm http://knowledgemap.mc.vanderbilt.edu/research/content/medex-tool-finding-medication-information
 
Questions:
1.  The i2b2 demo ontology is at the NDC level.  Is that what we should use and do a look up from our RxNorm CUI to a representative NDC?  Or, has someone developed another RxNorm CUI tree? 
2.  Do other places find that the i2b2 demo ontology covers most everything that people use in your medical center? 
3.  Do all the UCalifornia and Harvard sites run on this medication ontology?
 
If that's the case we might favor the NDC mapping over the GCNSEQNO.
 
Otherwise, we'd then need to create an ontology similar to what Recombinant did and now that NDF-RT is native in the UMLS this should be more straightforward.  Or, we could see if NCBO has a downloadable i2b2 compatible ontology.  Or, we could investigate things like this 3M announcement:  http://www.hddaccess.com/
 
We want to go the right way because we think if we bake our own ontology that may be problematic if the goal is to have search across institutions and have it work on concept paths as opposed to concept codes.  Otherwise, you can share data but the whole ontology concept path thing won't work unless we harmonize our paths across sites. 
For example our local ontology has Medications\Anticoagulants\Heparins  and Medications\Anticoagulants\Low Molecular Weight Heparins which are two concept paths likely unmeaningful to anyone else using i2b2.
 
Thank you for any guidance you can provide,
   
 
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 http://informatics.kumc.edu




Query resulting while selecting same financial encounter [06-26-2012]

Anchor
_MailOriginal
_MailOriginal
From: Mendis, Michael E. Sent: Tuesday, June 26, 2012 3:04 PMTo: Patibandla, NandanCc: i2b2 AUG Members
Subject: Re: Query resulting while selecting the same financial encounter
which server are you using?
mike

On Jun 26, 2012, at 2:55 PM, Patibandla, Nandan wrote:
Hi Mike,
I am getting this following error in the log file and the webclients just shows up as error when we select the option of "Occurs in the same encounter". Can you please let us know why this is happening

2012-06-26 14:51:42,160 DEBUG [edu.harvard.i2b2.crc.util.PMServiceAccountUtil] CRC using service account from property file [AGG_SERVICE_ACCOUNT]
2012-06-26 14:51:42,160 DEBUG [edu.harvard.i2b2.crc.dao.CRCDAO] Checking for valid query timing [SAMEVISIT] with panel timing [SAMEVISIT]
2012-06-26 14:51:42,160 DEBUG [edu.harvard.i2b2.crc.dao.CRCDAO] Checking for valid query timing [SAMEVISIT] with panel timing [SAMEINSTANCENUM]
2012-06-26 14:51:42,160 ERROR [STDERR] java.lang.IllegalStateException: BaseTransaction.rollback - [com.arjuna.ats.internal.jta.transaction.arjunacore.notx] [com.arjuna.ats.internal.jta.transaction.arjunacore.notx] no transaction!
2012-06-26 14:51:42,160 ERROR [STDERR] at com.arjuna.ats.internal.jta.transaction.arjunacore.BaseTransaction.rollback(BaseTransaction.java:158)
2012-06-26 14:51:42,160 ERROR [STDERR] at com.arjuna.ats.jbossatx.BaseTransactionManagerDelegate.rollback(BaseTransactionManagerDelegate.java:126)
2012-06-26 14:51:42,160 ERROR [STDERR] at edu.harvard.i2b2.crc.dao.setfinder.QueryExecutorDao.executeSQL(Unknown Source)
2012-06-26 14:51:42,160 ERROR [STDERR] at edu.harvard.i2b2.crc.ejb.ExecRunnable.processQueryRequest(Unknown Source)
2012-06-26 14:51:42,160 ERROR [STDERR] at edu.harvard.i2b2.crc.ejb.ExecRunnable.execute(Unknown Source)
2012-06-26 14:51:42,160 ERROR [STDERR] at edu.harvard.i2b2.crc.ejb.QueryExecutorMDB.onMessage(Unknown Source)
2012-06-26 14:51:42,160 ERROR [STDERR] at edu.harvard.i2b2.crc.ejb.QuerySmallExecutorMDB.onMessage(Unknown Source)
2012-06-26 14:51:42,160 ERROR [STDERR] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
2012-06-26 14:51:42,160 ERROR [STDERR] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
2012-06-26 14:51:42,160 ERROR [STDERR] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
2012-06-26 14:51:42,160 ERROR [STDERR] at java.lang.reflect.Method.invoke(Method.java:597)
2012-06-26 14:51:42,160 ERROR [STDERR] at org.jboss.invocation.Invocation.performCall(Invocation.java:359)
2012-06-26 14:51:42,160 ERROR [STDERR] at org.jboss.ejb.MessageDrivenContainer$ContainerInterceptor.invoke(MessageDrivenContainer.java:495)
2012-06-26 14:51:42,160 ERROR [STDERR] at org.jboss.resource.connectionmanager.CachedConnectionInterceptor.invoke(CachedConnectionInterceptor.java:158)
2012-06-26 14:51:42,160 ERROR [STDERR] at org.jboss.ejb.plugins.CallValidationInterceptor.invoke(CallValidationInterceptor.java:63)
2012-06-26 14:51:42,160 ERROR [STDERR] at org.jboss.ejb.plugins.AbstractTxInterceptor.invokeNext(AbstractTxInterceptor.java:121)
2012-06-26 14:51:42,160 ERROR [STDERR] at org.jboss.ejb.plugins.AbstractTxInterceptorBMT.invokeNext(AbstractTxInterceptorBMT.java:173)
2012-06-26 14:51:42,160 ERROR [STDERR] at org.jboss.ejb.plugins.MessageDrivenTxInterceptorBMT.invoke(MessageDrivenTxInterceptorBMT.java:47)
2012-06-26 14:51:42,160 ERROR [STDERR] at org.jboss.ejb.plugins.MessageDrivenInstanceInterceptor.invoke(MessageDrivenInstanceInterceptor.java:116)
2012-06-26 14:51:42,160 ERROR [STDERR] at org.jboss.ejb.plugins.RunAsSecurityInterceptor.invoke(RunAsSecurityInterceptor.java:109)
2012-06-26 14:51:42,160 ERROR [STDERR] at org.jboss.ejb.plugins.LogInterceptor.invoke(LogInterceptor.java:205)
2012-06-26 14:51:42,160 ERROR [STDERR] at org.jboss.ejb.plugins.ProxyFactoryFinderInterceptor.invoke(ProxyFactoryFinderInterceptor.java:138)
2012-06-26 14:51:42,160 ERROR [STDERR] at org.jboss.ejb.MessageDrivenContainer.internalInvoke(MessageDrivenContainer.java:402)
2012-06-26 14:51:42,160 ERROR [STDERR] at org.jboss.ejb.Container.invoke(Container.java:960)
2012-06-26 14:51:42,160 ERROR [STDERR] at org.jboss.ejb.plugins.jms.JMSContainerInvoker.invoke(JMSContainerInvoker.java:987)
2012-06-26 14:51:42,160 ERROR [STDERR] at org.jboss.ejb.plugins.jms.JMSContainerInvoker$MessageListenerImpl.onMessage(JMSContainerInvoker.java:1287)
2012-06-26 14:51:42,160 ERROR [STDERR] at org.jboss.jms.asf.StdServerSession.onMessage(StdServerSession.java:266)
2012-06-26 14:51:42,160 ERROR [STDERR] at org.jboss.mq.SpyMessageConsumer.sessionConsumerProcessMessage(SpyMessageConsumer.java:891)
2012-06-26 14:51:42,160 ERROR [STDERR] at org.jboss.mq.SpyMessageConsumer.addMessage(SpyMessageConsumer.java:170)
2012-06-26 14:51:42,160 ERROR [STDERR] at org.jboss.mq.SpySession.run(SpySession.java:323)
2012-06-26 14:51:42,160 ERROR [STDERR] at org.jboss.jms.asf.StdServerSession.run(StdServerSession.java:194)
2012-06-26 14:51:42,160 ERROR [STDERR] at EDU.oswego.cs.dl.util.concurrent.PooledExecutor$Worker.run(PooledExecutor.java:761)
2012-06-26 14:51:42,160 ERROR [STDERR] at java.lang.Thread.run(Thread.java:619)
Thank you
Nandan




Issues for 1.6.05 [06-25-2012]

From: Robert Schuff [schuffr.ohsu] Sent: Monday, June 25, 2012 12:53 AM To: Murphy, Shawn N.; i2b2 AUG Members Subject: Re: Issues for 1.6.05 ... WAS: Re: workbench default value
Hi Shawn,
Peter has the details but in short they are:
1)  Where/How to programmatically set the property for the number of Ontology items to display. edited for all the ontology properties.
Here's a copy of his original email:


From: Peter Beninato 
Sent: Friday, June 08, 2012 2:17 PM
To: 'Mendis, Michael E.'; i2b2 AUG Members
Subject: i2b2 - v1.6.x - Ontology - Maximum Number of Children to Display
 
Hi,
 
I noticed this in v1.6.03 and now in 1.6.04.
I want to set the property of Maximum Number of Children to Display to a high enough values to avoid the prompt.
In the past this was set in \webclient\js-i2b2\cells\ONT\cell_config_data.js.
I have set this value to 1000, however, in the webclient it still defaults to 200.
Additionally, I have set it in default.htm to 1000 here:
<div style="font-size:12px; margin-left:50px" >Maximum Number of Children to Display: <input id="ONTNAVMaxQryDisp" style="width:35px" value="1000" /></div>
 
And here:
<div style="font-size:12px; margin-left:50px" >Maximum Number of Children to Display: <input id="ONTFINDMaxQryDisp" style="width:35px" value="1000" /></div>
 
But that also does not seem to have an impact.
Please advise where to set this value.

2)    Ontology and Modifier codes optimization/timeout issue. In our tree, we have Ontology items that can have 1000s of items. On our DEV/TEST server, the Ontology cell times out and doesn't display ontology tree. Based on some tracing Peter has been doing, this seems related to all the Modifier Code Count queries that are being run. Thanks to Lori for mentioning the property to turn off Modifier Codes entirely, so now at least the tree can be displayed, but if I understand correctly, this is something that is done through a web client setting so each user has to set it.
Thanks for checking it out Shawn.
Rob
Robert Schuff, MS 
Instructor, Dept. of Medical Informatics and Clinical Epidemiology 
Director, Clinical Research Informatics
Oregon Clinical & Translational Research Institute Oregon Health & Science University

From: Peter Beninato [beninato.ohsu] Sent: Friday, June 22, 2012 5:13 PM To: Murphy, Shawn N.; Robert Schuff; i2b2 AUG Members Subject: RE: Issues for 1.6.05 ... WAS: Re: workbench default value
Hi,
Briefly:

Where/How to programmatically set the property for the number of Ontology items to display in the webclient. It defaults to 200, and is not responding to typical edits.
Make the file \webclient\js-i2b2\cells\ONT\cell_config_data.js be "the" file that needs to be edited for all the ontology properties.
Ontology and Modifier codes  optimization/timeout. In our tree, we have Ontology items that can have 1000s of items. On our DEV/TEST server, the Ontology cell times out and doesn't display ontology tree. This seems related to all the Modifier Code Count queries that are being run. Thanks to Lori for mentioning the property to turn off Modifier Codes entirely, so now at least the tree can be displayed. In the future we may want to use Modifier Codes, but need to be able have it  work with large ontologies.
Peter


From: "Murphy, Shawn N."
Date: Fri, 22 Jun 2012 12:45:34 -0700 To: Robert Schuff, i2b2 AUG Members Subject: RE: Issues for 1.6.05 ... WAS: Re: workbench default value
We can check, do you have them handy?
 
Thanks,
Shawn.


From: Robert Schuff Sent: Friday, June 22, 2012 3:14 PM To: Murphy, Shawn N.; i2b2 AUG Members Subject: Issues for 1.6.05 ... WAS: Re: workbench default value
Hi Shawn/Mike,
Do you have a list of those fixes?  We've identified one or two possible issues but we aren't yet sure if they have been recognized/addressed.  Peter has brought these up recently on the listserv.
Thanks!
Rob 
Robert Schuff, MS 
Instructor, Dept. of Medical Informatics and Clinical Epidemiology 
Director, Clinical Research Informatics
Oregon Clinical & Translational Research Institute Oregon Health & Science University

From: "Murphy, Shawn N."
Date: Fri, 22 Jun 2012 11:55:18 -0700 To: "'Wei,Xintao'" , i2b2 AUG Members Subject: RE: workbench default value
Good point Xintao, we have some minor fixes coming out as a 1.6.05 soon and we can see if others agree that would be a good idea for the release.  Also, if you want to dive into the code it should not be to bad!
 
Thanks,
Shawn.

From: Wei,Xintao Sent: Friday, June 22, 2012 11:16 AM To: i2b2 AUG Members Subject: workbench default value
Hi,
Is it possible to change the default "Analysis Types" on i2b2 workbench from "Timeline" to "Number of patients"? See the attached picture:

When opening a I2B2 workbench (1.6.02), the default value for "Analysis Types" on the "Query Tool" panel is "Timeline".  Can I change the default value to "Number of patients"? Because the DATA_OBFSC type of users don't have "Timeline" rights, they have to uncheck the "Timeline" option every time when opening the i2b2 workbench, otherwise the system will take longer time to return results.
Any suggestions? Thank you,
Xintao




i2b2 Authentication using LDAP [06-22-2012]
From: Jack London Sent: Friday, June 22, 2012 10:43 AM To: Peter Beninato; i2b2 AUG Members; Mendis, Michael E. Subject: Re: i2b2 authentication using LDAP
Hi Peter,
Yes, changing the "security_authentication" to "simple" solved the problem.
Thanks,
Jack

From: Peter Beninato Date: Thursday, June 21, 2012 5:20 PM To: Jack London, i2b2 AUG Members Subject: RE: i2b2 authentication using LDAP
Hi Jack,
 
I think your issue is related to the value for security_authentication. You may have it set to 'anonymous'. I fought this awhile ago, and from memory, I think that was it.
In the script attached it is set to 'simple', which I think is what you want.
 
(BTW, many thanks to Johnny Phan at UTH for this!)
 
Edit the script for the individual institutions values (see below)
 
You need to edit this is the script:
<<YOUR_LIST_OF_VALID_USERS>>
<<YOUR_LDAP_URL>>
<< OU=???,dc=?,dc=??,dc=?? >> ( this is for search base replace the question marks and I'm not sure you'll need all the dc's)
 
Peter
 
 
From: Jack London Sent: Thursday, June 21, 2012 1:12 PM To: i2b2 AUG Members Subject: i2b2 authentication using LDAP
 
I followed the directions on the i2b2 wiki document for setting the user parameters so that LDAP credentials are used.
 
For that user ANY text entered for the password is accepted and access to the i2b2 web client is granted.  (For all other users, you must enter a correct password corresponding to the value in the i2b2 PM table.)
 
What did I do wrong?
 
thanks ...
 
Jack
 




i2b2 – v1.6x – Ontology – Maximum Number of Children to Display – Web Client [06-21-2012]
From: Peter Beninato [beninato.ohsu] Sent: Thursday, June 21, 2012 6:33 PM To: i2b2 AUG Members Subject: FW: i2b2 - v1.6.x - Ontology - Maximum Number of Children to Display --> webclient
Hi,
See prior post from below.
The property in ...\ONT\cell_config_data.js, and in default.htm do not seem to set the value.
It defaults to 200, and they are set it to 1,000.
Thanks.
Peter

From: Peter Beninato Sent: Friday, June 08, 2012 2:17 PM To: 'Mendis, Michael E.'; i2b2 AUG Members Subject: i2b2 - v1.6.x - Ontology - Maximum Number of Children to Display
Hi,
I noticed this in v1.6.03 and now in 1.6.04.
I want to set the property of Maximum Number of Children to Display to a high enough values to avoid the prompt.
In the past this was set in \webclient\js-i2b2\cells\ONT\cell_config_data.js.
I have set this value to 1000, however, in the webclient it still defaults to 200.
Additionally, I have set it in default.htm to 1000 here:
<div style="font-size:12px; margin-left:50px" >Maximum Number of Children to Display: <input id="ONTNAVMaxQryDisp" style="width:35px" value="1000" /></div>
And here:
<div style="font-size:12px; margin-left:50px" >Maximum Number of Children to Display: <input id="ONTFINDMaxQryDisp" style="width:35px" value="1000" /></div>
But that also does not seem to have an impact.
Please advise where to set this value.
Thanks.
Peter Beninato - OCTRI DW Developer
Oregon Health & Science University
503-494-9985




Question about i2b2 de-identification [06-19-2012]
From:Murphy, Shawn N.
Sent:Tuesday, June 19, 2012 9:37 AM
To:Hogan, William R; i2b2 AUG Members
Subject:RE: Question about i2b2 de-identification
Hi Bill,
They are generated by AES encryption in the import plug-in, please see the "Import plug-in help" guide.
Thanks,
Shawn.

From: Hogan, William R [WRHogan.uams]
Sent: Tuesday, June 12, 2012 11:13 AM
To: i2b2 AUG Members
Subject: Question about i2b2 de-identification
I am looking for documentation about how i2b2 generates the identifiers it puts in place of MRNs, etc.
Does any such documentation exist? If not, does anyone know how it generates them?
Bill




i2b2 – v1.6x – Ontology – Maximum Number of Children to Display – Web Client [06-19-2012]

From: Murphy, Shawn N. Sent: Tuesday, June 19, 2012 9:31 AM To: Peter Beninato; Mendis, Michael E.; i2b2 AUG Members; Phillips, Lori C. Subject: RE: i2b2 - v1.6.x - Ontology - Maximum Number of Children to Display
Lori is on vacation Peter, and she owns the Ontology Cell.  She'll be able to address your questions next week.
Thanks,
Shawn.

From: Peter Beninato [beninato.ohsu] Sent: Tuesday, June 12, 2012 2:00 PM To: Peter Beninato; Mendis, Michael E.; i2b2 AUG Members Subject: RE: i2b2 - v1.6.x - Ontology - Maximum Number of Children to Display
Hi,
Still not sure where to set property programmatically (original email below ...---... help),
But also, when I expand ontology item with a lot of leaves, doesn't ever seem to resolve.
When I look at the JBOSS server.log, I see entries like below. Now clearly I have DEBUG on which can impact performance (on a VM on a shared server too)
, but it seems interesting that this SQL (or SQL very much like below) is getting run iteratively on the ontology path, even after the session is over.
What does this do? Run a count for modifier codes?
All m_applied_path(s) are set to the "@" character.
Is it possible to turn it off, if you are not using modifier codes?
Thanks.
Peter

2012-06-12 10:43:53,810 DEBUG [org.springframework.jdbc.datasource.DataSourceUtils] Fetching JDBC Connection from DataSource
2012-06-12 10:44:01,815 DEBUG [org.springframework.jdbc.datasource.DataSourceUtils] Returning JDBC Connection to DataSource
2012-06-12 10:44:01,815 DEBUG [org.springframework.jdbc.core.JdbcTemplate] Executing SQL query [
select count(star)
from octrii2b2meta.i2b2
where m_exclusion_cd is null
and c_fullname in(select c_fullname
                  from octrii2b2meta.i2b2
                  where c_hlevel = 1
                  and m_exclusion_cd is null
                  and (m_applied_path = '\i2b2\Meds\UNCLASSIFIED\UNCLASSIFIED\AMPHOTERICIN B LIPID COMPLEX (ABELCET) IV (TEST DOSE)_4001016\'
                       or m_applied_path = '\i2b2\Meds\UNCLASSIFIED\UNCLASSIFIED\AMPHOTERICIN B LIPID COMPLEX (ABELCET) IV (TEST DOSE)_4001016%'
                       or m_applied_path = '\i2b2\Meds\UNCLASSIFIED\UNCLASSIFIED%' or m_applied_path = '\i2b2\Meds\UNCLASSIFIED%'
                       or m_applied_path = '\i2b2\Meds%' or m_applied_path = '\i2b2%' or m_applied_path = '%'
                       )
                  MINUS 
                  (select c_fullname
                   from   octrii2b2meta.i2b2
                   where m_exclusion_cd is not null
                   and (
                         m_applied_path = '\i2b2\Meds\UNCLASSIFIED\UNCLASSIFIED\AMPHOTERICIN B LIPID COMPLEX (ABELCET) IV (TEST DOSE)_4001016\'
                        or m_applied_path = '\i2b2\Meds\UNCLASSIFIED\UNCLASSIFIED\AMPHOTERICIN B LIPID COMPLEX (ABELCET) IV (TEST DOSE)_4001016%'
                   or m_applied_path = '\i2b2\Meds\UNCLASSIFIED\UNCLASSIFIED%'
                   or m_applied_path = '\i2b2\Meds\UNCLASSIFIED%'
                   or m_applied_path = '\i2b2\Meds%' or m_applied_path = '\i2b2%' or m_applied_path = '%'
                        )
                   )
                 )]

From: Peter Beninato Sent: Friday, June 08, 2012 2:17 PM To: 'Mendis, Michael E.'; i2b2 AUG Members Subject: i2b2 - v1.6.x - Ontology - Maximum Number of Children to Display
Hi,
I noticed this in v1.6.03 and now in 1.6.04.
I want to set the property of Maximum Number of Children to Display to a high enough values to avoid the prompt.
In the past this was set in \webclient\js-i2b2\cells\ONT\cell_config_data.js.
I have set this value to 1000, however, in the webclient it still defaults to 200.
Additionally, I have set it in default.htm to 1000 here:
<div style="font-size:12px; margin-left:50px" >Maximum Number of Children to Display: <input id="ONTNAVMaxQryDisp" style="width:35px" value="1000" /></div>
And here:
<div style="font-size:12px; margin-left:50px" >Maximum Number of Children to Display: <input id="ONTFINDMaxQryDisp" style="width:35px" value="1000" /></div>
But that also does not seem to have an impact.
Please advise where to set this value.
Thanks.
Peter Beninato - OCTRI DW Developer
Oregon Health & Science University
503-494-9985



i2b2 – v1.6.04 – Modifier Codes – ontology columns [06-15-2012]
From: Peter Beninato [beninato.ohsu] Sent: Friday, June 15, 2012 1:35 PM To: i2b2 AUG Members Subject: i2b2 - v1.6.04 - Modifier Codes - ontology columnns
Hi,
Sent email earlier about the query that is running related to modifier codes.
If anyone replied to that email, the firewall might have suppressed it, if it contained XML.
Some sample SQL scraped from the JBOSS server log is below.
There is criteria about m_exclusion_cd is null, at the top-level
I hoping to set this column to a non-null character to at least short-circuit the result to no rows, unless there is a different way to manage this.
However, upon reviewing the Ontology_Design_doc.pdf, the entry for m_exclusion_cd on page 13:
Traditional concept terms and non-exclusion modifiers have an
m_exclusion_cd of null. An m_applied_path of '\Diagnoses\Circulatory system%'
and m_exclusion_cd of 'X' means that the term is a modifier that is excluded
So, I'd like to set the value to 'X' to short-circuit, but the documentation say that "Traditional concept terms should set this the NULL."
Perhaps the documentation should read that Traditional concept terms should also be set to 'X'?

2012-06-15 09:22:16,937 DEBUG [org.springframework.jdbc.core.JdbcTemplate]
Executing SQL query [
select count(star)
 from octrii2b2meta.i2b2
 where m_exclusion_cd is null
 and c_fullname in (
                    select c_fullname
                    from octrii2b2meta.i2b2
                    where c_hlevel = 1
                    and m_exclusion_cd is null
                    and (
                           m_applied_path = '\i2b2\Meds\ANTICONVULSANTS\ANTICONVULSANT - CARBOXYLIC ACID DERIVATIVES\DEPAKENE ORAL_84549\'
                        or m_applied_path = '\i2b2\Meds\ANTICONVULSANTS\ANTICONVULSANT - CARBOXYLIC ACID DERIVATIVES\DEPAKENE ORAL_84549%'
                        or m_applied_path = '\i2b2\Meds\ANTICONVULSANTS\ANTICONVULSANT - CARBOXYLIC ACID DERIVATIVES%'
                        or m_applied_path = '\i2b2\Meds\ANTICONVULSANTS%'
                        or m_applied_path = '\i2b2\Meds%'
                        or m_applied_path = '\i2b2%'
                        or m_applied_path = '%' )
                    MINUS 
                    (
                     select c_fullname
                     from octrii2b2meta.i2b2
                     where m_exclusion_cd is not null
                     and (
                           m_applied_path = '\i2b2\Meds\ANTICONVULSANTS\ANTICONVULSANT - CARBOXYLIC ACID DERIVATIVES\DEPAKENE ORAL_84549\'
                        or m_applied_path = '\i2b2\Meds\ANTICONVULSANTS\ANTICONVULSANT - CARBOXYLIC ACID DERIVATIVES\DEPAKENE ORAL_84549%'
                        or m_applied_path = '\i2b2\Meds\ANTICONVULSANTS\ANTICONVULSANT - CARBOXYLIC ACID DERIVATIVES%'
                        or m_applied_path = '\i2b2\Meds\ANTICONVULSANTS%'
                        or m_applied_path = '\i2b2\Meds%' or m_applied_path = '\i2b2%'
                        or m_applied_path = '%' )))]
Peter Beninato - OCTRI DW Developer
Oregon Health & Science University
503-494-9985



Provider Query [06-14-2012]
From: Schulte, Gregory [Gregory.Schulte.childrenscolorado] Sent: Thursday, June 14, 2012 11:45 AM To: 'Lisa Miao'; i2b2 AUG Members Subject: RE: provider query
Lisa,
Can you check your i2b2 table to see what you have populated in the "C_FACTTABLECOLUMN" column for providers data.
"select C_FACTTABLECOLUMN from i2b2metadata.i2b2 where c_fullname like '\i2b2\Providers%'"
It should be "provider_id" and not "encounter_num"
Greg

From: Lisa Miao Sent: Thursday, June 14, 2012 9:01 AM To: i2b2 AUG Members Subject: provider query
Dear i2b2 team,
Following is the provider query that is being executed in i2b2 when we move a provider node to the right panel to query.
Does provider_dimension have a encounter_num field? We are running 1.6.02. We have run the i2b2createdb-1602.zip for our database. I do NOT see provider_dimension table have encounter_num field. Am I missing something?
Thanks,
Lisa.

select patient_num from observation_fact where
((   encounter_num IN (select encounter_num from provider_dimension    where provider_path like '\i2b2\Providers\Emergency Medical Service Providers%')      ))
 ) allitem ;




Offerings on i2b2 community web site [06-12-2012]
From: Murphy, Shawn N. Sent: Tuesday, June 12, 2012 10:54 PM To: i2b2 AUG Members Subject: Offerings on i2b2 community web site
Hi All,
We have two fairly complete products to offer on the community web site.
The first is the SMART-i2b2 product (Substitutable Medical Apps and Reusable Technologies) which allows the web client to be used to view single patient medical records when the user has limited data set privileges or better.  It consists of two new cells and a web client plug-in that functions with any Hive that is 1.5 or greater.  It is available at:https://community.i2b2.org/wiki/display/SMArt
The second is the mi2b2 product (medical imaging informatics biology to the bedside) which allows DICOM images to be retrieved from the PACS.  It consists of a new cell and a Workbench plug-in that functions with any HIVE that is 1.5 or greater.  It is available at:https://community.i2b2.org/wiki/display/mi2b2
The SMART plug-in has a Google Group for SMART-i2b2 Help questions at https://groups.google.com/d/forum/smart-i2b2
Both have Videos to demonstrate the products, and both are available under the i2b2 open source license.
Thanks,
Shawn.




Occurs > 1 Query [06-12-2012]
From: Mendis, Michael E. Sent: Tuesday, June 12, 2012 1:20 PMTo: Lisa MiaoCc: i2b2 AUG MembersSubject: Re: occurs > 1 query
This was an error that was resolved in 1.6.03
sorry bout it.
mike

On Jun 12, 2012, at 1:17 PM, Lisa Miao wrote:
Has anyone been able to successfully execute a query that has "occurs > 1" (in the constraint panel)?
I am getting the following "Error while executing sql" error. We are using 1.6.02. Not sure if this has been fixed in later release or not.
Thanks,
Lisa.

2012-06-12 13:15:07,299 ERROR [edu.harvard.i2b2.crc.ejb.ExecRunnable] Error while executing sql
edu.harvard.i2b2.common.exception.I2B2DAOException: Error while executing sql
at edu.harvard.i2b2.crc.dao.setfinder.QueryExecutorHelperDao.executeQuery(Unknown Source)
at edu.harvard.i2b2.crc.dao.setfinder.QueryExecutorDao.executeSQL(Unknown Source)
at edu.harvard.i2b2.crc.ejb.ExecRunnable.processQueryRequest(Unknown Source)
at edu.harvard.i2b2.crc.ejb.ExecRunnable.execute(Unknown Source)
at edu.harvard.i2b2.crc.ejb.QueryExecutorMDB.onMessage(Unknown Source)
at edu.harvard.i2b2.crc.ejb.QuerySmallExecutorMDB.onMessage(Unknown Source)
at sun.reflect.GeneratedMethodAccessor480.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.jboss.invocation.Invocation.performCall(Invocation.java:359)
at org.jboss.ejb.MessageDrivenContainer$ContainerInterceptor.invoke(MessageDrivenContainer.java:495)
at org.jboss.resource.connectionmanager.CachedConnectionInterceptor.invoke(CachedConnectionInterceptor.java:158)
at org.jboss.ejb.plugins.CallValidationInterceptor.invoke(CallValidationInterceptor.java:63)
at org.jboss.ejb.plugins.AbstractTxInterceptor.invokeNext(AbstractTxInterceptor.java:121)
at org.jboss.ejb.plugins.AbstractTxInterceptorBMT.invokeNext(AbstractTxInterceptorBMT.java:173)
at org.jboss.ejb.plugins.MessageDrivenTxInterceptorBMT.invoke(MessageDrivenTxInterceptorBMT.java:47)
at org.jboss.ejb.plugins.MessageDrivenInstanceInterceptor.invoke(MessageDrivenInstanceInterceptor.java:116)
at org.jboss.ejb.plugins.RunAsSecurityInterceptor.invoke(RunAsSecurityInterceptor.java:109)
at org.jboss.ejb.plugins.LogInterceptor.invoke(LogInterceptor.java:205)
at org.jboss.ejb.plugins.ProxyFactoryFinderInterceptor.invoke(ProxyFactoryFinderInterceptor.java:138)
at org.jboss.ejb.MessageDrivenContainer.internalInvoke(MessageDrivenContainer.java:402)
at org.jboss.ejb.Container.invoke(Container.java:960)
at org.jboss.ejb.plugins.jms.JMSContainerInvoker.invoke(JMSContainerInvoker.java:987)
at org.jboss.ejb.plugins.jms.JMSContainerInvoker$MessageListenerImpl.onMessage(JMSContainerInvoker.java:1287)
at org.jboss.jms.asf.StdServerSession.onMessage(StdServerSession.java:266)
at org.jboss.mq.SpyMessageConsumer.sessionConsumerProcessMessage(SpyMessageConsumer.java:891)
at org.jboss.mq.SpyMessageConsumer.addMessage(SpyMessageConsumer.java:170)
at org.jboss.mq.SpySession.run(SpySession.java:323)
at org.jboss.jms.asf.StdServerSession.run(StdServerSession.java:194)
at EDU.oswego.cs.dl.util.concurrent.PooledExecutor$Worker.run(PooledExecutor.java:761)
at java.lang.Thread.run(Thread.java:619)
Caused by: java.sql.SQLException: ORA-00905: missing keyword
at oracle.jdbc.driver.DatabaseError.throwSqlException(DatabaseError.java:112)
at oracle.jdbc.driver.T4CTTIoer.processError(T4CTTIoer.java:331)
at oracle.jdbc.driver.T4CTTIoer.processError(T4CTTIoer.java:288)
at oracle.jdbc.driver.T4C8Oall.receive(T4C8Oall.java:743)
at oracle.jdbc.driver.T4CStatement.doOall8(T4CStatement.java:207)
at oracle.jdbc.driver.T4CStatement.executeForRows(T4CStatement.java:946)
at oracle.jdbc.driver.OracleStatement.doExecuteWithTimeout(OracleStatement.java:1168)
at oracle.jdbc.driver.OracleStatement.executeUpdateInternal(OracleStatement.java:1614)
at oracle.jdbc.driver.OracleStatement.executeUpdate(OracleStatement.java:1579)
at org.jboss.resource.adapter.jdbc.WrappedStatement.executeUpdate(WrappedStatement.java:186)
... 31 more




i2b2 Server Hang [06-11-2012]
From: Lisa Miao [lmiao.regenstrief] Sent: Monday, June 11, 2012 10:47 AMTo: Mendis, Michael E.; Lisa MiaoCc: i2b2 AUG MembersSubject: RE: i2b2 server hang
We are using 1.6.02.
I was running the utility to update all the counts on the term tree.
Thanks,
Lisa.

From: Mendis, Michael E. [MMENDIS.PARTNERS]
Sent: Monday, June 11, 2012 10:46 AM
To: Lisa Miao
Cc: i2b2 AUG Members
Subject: Re: i2b2 server hang
Which version of i2b2 was this? was anything going on prior to this message coming up. such as a large load or lots of queries?
mike

On Jun 11, 2012, at 10:02 AM, Lisa Miao wrote:
Dear i2b2 team,
Just want to report, I have the following messages in the server.log, and the server is hanging. Shutdown.sh won't kill the server either. If anyone has run into this and has explanation, please share.
Thanks,
Lisa.

2012-06-11 05:42:18,125 WARN [org.jboss.mq.il.uil2.UILServerILService] Failed to setup client connection
java.net.SocketException: Too many open files
at java.net.PlainSocketImpl.socketAccept(Native Method)
at java.net.PlainSocketImpl.accept(PlainSocketImpl.java:390)
at java.net.ServerSocket.implAccept(ServerSocket.java:453)
at java.net.ServerSocket.accept(ServerSocket.java:421)
at org.jboss.mq.il.uil2.UILServerILService.run(UILServerILService.java:159)
at java.lang.Thread.run(Thread.java:619)
2012-06-11 05:42:18,125 WARN [org.jboss.mq.il.uil2.UILServerILService] Failed to setup client connection
java.net.SocketException: Too many open files
at java.net.PlainSocketImpl.socketAccept(Native Method)
at java.net.PlainSocketImpl.accept(PlainSocketImpl.java:390)
at java.net.ServerSocket.implAccept(ServerSocket.java:453)
at java.net.ServerSocket.accept(ServerSocket.java:421)
at org.jboss.mq.il.uil2.UILServerILService.run(UILServerILService.java:159)
at java.lang.Thread.run(Thread.java:619)
2012-06-11 05:42:18,125 WARN [org.jboss.mq.il.uil2.UILServerILService] Failed to setup client connection
java.net.SocketException: Too many open files
at java.net.PlainSocketImpl.socketAccept(Native Method)
at java.net.PlainSocketImpl.accept(PlainSocketImpl.java:390)
at java.net.ServerSocket.implAccept(ServerSocket.java:453)
at java.net.ServerSocket.accept(ServerSocket.java:421)
at org.jboss.mq.il.uil2.UILServerILService.run(UILServerILService.java:159)
at java.lang.Thread.run(Thread.java:619)
2012-06-11 05:42:18,125 WARN [org.jboss.mq.il.uil2.UILServerILService] Failed to setup client connection
java.net.SocketException: Too many open files
at java.net.PlainSocketImpl.socketAccept(Native Method)
at java.net.PlainSocketImpl.accept(PlainSocketImpl.java:390)
at java.net.ServerSocket.implAccept(ServerSocket.java:453)
at java.net.ServerSocket.accept(ServerSocket.java:421)




Annual AUG Meeting [06-08-2012]

From: Churchill, Susanne E. Sent: Friday, June 08, 2012 2:50 PM To: i2b2 AUG Members Subject: Annual AUG Meeting
Dear Colleagues,
This is a reminder that our second Annual Boston-based i2b2 AUG Meeting is fast approaching:  July 24-25, 2012 (NLP Workshop in the morning of the 24th, i2b2 meeting noon on the 24th to noon on the 25th).
The agenda is as follows (and will be up in more detail on your web page shortly):
July 24 (afternoon):  Lunch; i2b2 v.1.7 Workshop; Community engagement (POSTER SESSION); Reception.
July 25 (morning):  Updates/discussion on i2b2-SMART, SHRINE-CT (Clinical Trials), GARLIC (Genomics Cell), ++
Lodging info available on your web page:  www.i2b2.org/work/aug.html.
1.  If you have not already let me know you'll be attending, please do so and specify NLP Workshop and/or the AUG Meeting. NO REGISTRATION FEE.
2,  PLEASE PLAN ON BRINGING A POSTER - THIS WAS A VERY POPULAR NETWORKING OPPORTUNITY LAST YEAR.  LET ME KNOW IF YOU WILL DO SO.
2.  We have a little play in the agenda, please let us know if you have requests.
3.  No programmed dinner this year, we thought you'd like to enjoy Boston dining in the summer.
Please let me know if you have any questions.  We look forward to seeing you.
Regards,
Susanne
Susanne E. Churchill, Ph.D. Executive Director i2b2/Nat'l Center for Biomedical Computing 77 Avenue Louis Pasteur, Room 255 Boston, MA 02115



Timeout Configurable [06-06-2012]
From: Mendis, Michael E. Sent: Wednesday, June 06, 2012 9:30 AMTo: Lisa Miao; i2b2 AUG MembersSubject: Re: timeout configurable?
Take a look at
js-i2b2/i2b2_cell_communcation.js (line 141)
Change the 180 (seconds) to a higher number
mike

On Jun 4, 2012, at 10:01 AM, Lisa Miao wrote:
Can you give me a pointer on how/where I can change the code?
This, I imagine, will be an important feature to add. Is this in the plan for future release?
Thanks,
Lisa.

From: Mendis, Michael E. [MMENDIS.PARTNERS]
Sent: Monday, June 04, 2012 9:59 AM
To: Lisa Miao; i2b2 AUG Members
Subject: RE: timeout configurable?
In both the webclient and workbench, you can change the timeout from the client, but both will require modifing the code.
Also once a request timeout, the query is still running and you can access the result from the previous query.
mike
From: Lisa Miao [lmiao.regenstrief]
Sent: Monday, June 04, 2012 9:35 AM
To: i2b2 AUG Members
Subject: timeout configurable?
Dear i2b2 team,
It seems like the "out of the box" behavior on executing an query has a timeout of 2min. Is this configurable?
We have a project that will have over 800 million records in observation_fact table. 2min query is not always be achievable.
Thanks,
Lisa.




Providing de-identified notes as part of i2b2 [06-05-2012]
From: Graciela Gonzalez Sent: Tuesday, June 05, 2012 12:38 PM To: Marsolo, Keith Cc: i2b2 AUG Members Subject: Re: Providing de-identified notes as part of i2b2
Hi Keith, Perhaps the MIST group has some pointers? (http://mist-deid.sourceforge.net/), particularly given their work published in JAMIA, Effects of personal identifier resynthesis on clinical text de-identification (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3000784/), where they include statistics of de-identification... They must have gone through a similar IRB processBest,GracielaDr. Graciela GonzalezAssistant ProfessorArizona State UniversityDepartment of Biomedical InformaticsMayo Clinic, Samuel C. Johnson Research Bldg13212 East Shea BoulevardScottsdale, AZ 85259
On Tue, Jun 5, 2012 at 7:24 AM, Marsolo, Keith wrote:
Has anyone been through the process of adding de-identified notes into their production i2b2 warehouse?  More specifically, the IRB process that would these notes to be given out as part of a "standard" extract?
I'm not talking about the effort to create a pipeline/algorithm for de-identification.  We've already got a protocol that allowed us to do that work.  What we're interested in is the next step - how do you write the protocol to put that pipeline into production?  The Cincinnati Children's IRB is asking us to demonstrate that our algorithm leaves the notes statistically de-identified.  We're wondering if anyone has been through this process, and if so, what approach they used to "prove" de-identification.  We've come up with a method, but it's always good to get a second opinion.
Thanks.
Keith
Keith Marsolo, PhDAssistant ProfessorDirector, Software Development & Data Warehouse
Division of Biomedical InformaticsCincinnati Children's Hospital Medical Center3333 Burnet AveMLC 7024Cincinnati, OH 45229



i2b2 1.6.04 and wizard.sh released [06-01-2012]
From: Mauro Bucalo [mauro.bucalo.gmail] Sent: Friday, June 01, 2012 6:29 AMTo: Sebastian MateCc: i2b2 AUG MembersSubject: Re: i2b2 1.6.04 is released
The wizard.sh is saved in Windows mode, converting in unix-linux mode it works well!!!
2012/5/31 Sebastian Mate <Sebastian.Mate.imi.med.uni-erlangen.de>:
Hi Mauro,
the problem is the encoding of the script file. Try to open it with Notepad++ and convert it to UTF-8, then it should work ...
I will fix this in the next version, which will hopefully be compatible with the new Ubuntu 12.04 LTS. I'm experiencing some issues with PHP, but I'm working on it.
Sebastian

Von: Mauro Bucalo
Gesendet: Montag, 28. Mai 2012 16:01
An: Sebastian Mate
Betreff: Re: i2b2 1.6.04 is released
The strange thing is that I use the 10.04.4 ubuntu desktop and up to the previous version the wizard works well !
I can try to retry the whole procedure..

2012/5/28 Sebastian Mate <Sebastian.Mate.imi.med.uni-erlangen.de>
Hi Mauro,
which Linux are you using? The wizard is designed for Ubuntu 10.04 and
definitely needs some small modifications if you're using a different Linux.
I haven't tested it with Ubuntu 12.04 yet, but I will do this next week.
Also make sure you're using bash as your shell ...
Maybe it helps if you launch it this way:
chmod +x wizard.sh./wizard.sh
Sebastian

Am 28.05.2012 um 12:20 schrieb Mauro Bucalo:

Hi Sebastian, launching the wizard i've found this error:
root@i2b2test:~/Public/i2b2wizard-1.4.2#sh wizard.sh
not found2:
not found5:
not found7:
not found9:
not found12:
not found15:
not found18:
not found20:
not found23:
wizard.sh: 141: Syntax error: word unexpected (expecting "do")
you know anything about that?
many thanks
2012/5/23 Sebastian Mate <Sebastian.Mate.imi.med.uni-erlangen.de>
... and a new version of i2b2 Wizard for it can be found here:http://www.imi.med.uni-erlangen.de/~matesn/i2b2wizard/
Make sure to pick version 1.4.2, which supports i2b2 1.6.04. It was only superficially tested, but it seems to work fine ...
J
Cheers
Sebastian
Dipl.-Inf. Sebastian Mate
Friedrich-Alexander-University of Erlangen-Nuremberg
Department for Medical Informatics
Krankenhausstrasse 12, 91054 ERLANGEN, GERMANY

Von: i2b2 AUG Members
von Murphy, Shawn N.
Gesendet: Mittwoch, 23. Mai 2012 13:30
An: i2b2 AUG Members
Betreff: i2b2 1.6.04 is released
This release does not contain any new features from 1.6.03, just some software fixes. Please see release notes for their description.
Thanks,
Shawn.