AUG Email 2012-Jun

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

From: Mendis, Michael E. Sent: Tuesday, June 26, 2012 3:04 PMTo: Patibandla, NandanCc: i2b2 AUG Members
while selecting the same financial encounter Patibandla, Nandan wrote: 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 [edu.harvard.i2b2.crc.util.PMServiceAccountUtil] CRC using service account from property file [AGG_SERVICE_ACCOUNT]
[edu.harvard.i2b2.crc.dao.CRCDAO] Checking for valid query timing [SAMEVISIT] with panel timing [SAMEVISIT]
[edu.harvard.i2b2.crc.dao.CRCDAO] Checking for valid query timing [SAMEVISIT] with panel timing [SAMEINSTANCENUM]
[STDERR] java.lang.IllegalStateException: BaseTransaction.rollback - [com.arjuna.ats.internal.jta.transaction.arjunacore.notx] [com.arjuna.ats.internal.jta.transaction.arjunacore.notx] no transaction!
at com.arjuna.ats.internal.jta.transaction.arjunacore.BaseTransaction.rollback(BaseTransaction.java:158)
at com.arjuna.ats.jbossatx.BaseTransactionManagerDelegate.rollback(BaseTransactionManagerDelegate.java:126)
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.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
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)

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
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
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 ;