AUG Email 2011-Jun

Last Updated: 06/30/2011

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From: Davis, Michael (Oncology) [davismk.upmc] Sent: Thursday, June 30, 2011 8:48 AM To: Murphy, Shawn N.; i2b2 AUG Members Subject: RE: Observation Set No longer returns
I'm using the DEMO account with: user, De-identified data, limited data set, aggregated, obfuscated, editor. Btw: In the Jboss console I see the observation query being executed without any errors.
Thx,
Mike

From: Murphy, Shawn N. [SNMURPHY.PARTNERS] Sent: Wednesday, June 29, 2011 2:58 PM To: Davis, Michael (Oncology); i2b2 AUG Members Subject: RE: Observation Set No longer returns
What are the data permissions for your login Mike?
Thanks,
Shawn.

From: Davis, Michael (Oncology) [davismk.upmc] Sent: Monday, June 27, 2011 11:33 AM To: i2b2 AUG Members Subject: Observation Set No longer returns
I was testing the PDO Analysis Tools in v 1.6 (web client) and noticed it does not return the observation_set anymore in the PDO response, even though this is checked as an option. The events and patients are returned correctly in the response. I used the following from demo data:
ns2:observation_set panel_name="\\BIRN\BIRN\oasis\Clinical Measures\Clinical Dementia Rating (CDR)\mild dementia\" /
Are there any special permissions needed now to view the observation data? Has anyone else encountered this problem?
Regards,
Mike


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From: Mendis, Michael E. Sent: Wednesday, June 29, 2011 1:10 PM To: Murphy, Shawn N.; Russ Waitman; Haijun Qiu; i2b2 AUG MembersSubject: Re: openldap user authentication
I have refactored the code for rc4, that it now contains a interface called SecurityAuthentication I created a class called SecurityAuthenticationNTLM and extended the interface to deal with NTLM calls. Any parameters that are needed such as domain for NTLM, would be in a param similar to the screenshot below. We can easy create a another class for CAS. I looked at the ticket but did not see any code, if you have some code I can transform to the class and we can try it out.
mike

On 6/21/11 9:37 AM, "Murphy, Shawn N." SNMURPHY.PARTNERS wrote:
I think Mike put either Dan's or Phillips's implementation into the 1.6 upcoming RC4 release as well, accessible through the PM Navigation...
Thanks,
Shawn.
From: Russ Waitman [rwaitman.kumc] Sent: Monday, June 06, 2011 4:43 PM To: Haijun Qiu; i2b2 AUG MembersSubject: Re: openldap user authentication
Hiajun,
Dan Connolly here did CAS integration as that was KUMC's single sign on solution. I think he's put our code hooks between i2b2 and CAS up on our TRAC website. The ticket that discusses the work is at:
http://informatics.kumc/work/ticket/8
Russ Waitman Associate Professor Director of Medical Informatics Department of Biostatistics University of Kansas Medical Center 913?945?7087 rwaitman.kumc http://informatics.kumc http://informatics.kumc/

"Qiu, Haijun" QIUH.email.chop 6/6/2011 1:09 PM
Hello,
Does anybody know what it takes to support openldap user authentication in i2b2. Which source and configuration files to modify? Link to some detailed documentation? We are looking into letting users use their openldap credentials to login into i2b2. We are currently running i2b2 1.5.
If openldap is still not supported, some documentation on Windows Active Directory sign?on will also help us to understand how much efforts may require to eventually support single sign?on.
Thanks,
Haijun Qiu Bioinformatics Scientist Center for Applied Genomics The Children's Hospital of Philadelphia Phone: (267)426?1257 Email: qiuh.email.chop


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From: Dat Q. Phan [Dat.Q.Phan.uth.tmc] Sent: Tuesday, June 28, 2011 4:57 PM To: Mendis, Michael E. Cc: Phillip Reeder; i2b2 AUG MembersSubject: RE: i2b2metadata.table_access Error
Yes, I installed it on two separate systems just to make sure.
Thanks Mike!

From: Mendis, Michael E. [MMENDIS.PARTNERS] Sent: Tuesday, June 28, 2011 3:54 PM To: Dat Q. Phan Cc: Phillip Reeder; i2b2 AUG MembersSubject: RE: i2b2metadata.table_access Error
So you did a fresh install of the rc3 data? Let me take a look at the demodata and get back to you.
mike

From: Dat Q. Phan [Dat.Q.Phan.uth.tmc] Sent: Tue 6/28/2011 4:36 PM To: Mendis, Michael E. Cc: Phillip Reeder; i2b2 AUG MembersSubject: RE: i2b2metadata.table_access Error
No, this error doesn't show up in the VM image. There is no "i2b2" under c_table_cd in the TABLE_ACCESS table. I think the error is in the demodata. When I tried to redirect the VM image to point to my Oracle demodata on a separate server I get the same error.

From: Mendis, Michael E. [MMENDIS.PARTNERS] Sent: Tuesday, June 28, 2011 3:26 PM To: Dat Q. Phan Cc: Phillip Reeder; i2b2 AUG MembersSubject: RE: i2b2metadata.table_access Error
Was this on the vm image? But it should have a entry with the i2b2 entry in the table_access. Which is why the error 'Incorrect result size: expected 1, actual 0'
I am hoping to get rc4 out soon, doing a extensive qa on it now.
mike

From: Dat Q. Phan [Dat.Q.Phan.uth.tmc] Sent: Tue 6/28/2011 4:13 PM To: Mendis, Michael E. Cc: Phillip Reeder; i2b2 AUG MembersSubject: i2b2metadata.table_access Error
Mike,
I'm running i2b2 v1.6 RC3 and I get an error (see attached: Query Errors.png) when I run a query in the demodata with all the query result types checked (see attached: Query Result Types.png).
Below is the error in server.log:
2011-06-20 12:14:49,702 DEBUG [org.springframework.jdbc.core.JdbcTemplate] Executing SQL query [select distinct(c_table_name) from demodata.table_access where c_table_cd = ? and c_protected_access = ? ] 2011-06-20 12:14:49,702 DEBUG [org.springframework.jdbc.datasource.DataSourceUtils] Fetching JDBC Connection from DataSource 2011-06-20 12:14:49,702 DEBUG [org.springframework.jdbc.core.StatementCreatorUtils] Setting SQL statement parameter value: column index 1, parameter value [i2b2], value class [java.lang.String], SQL type unknown 2011-06-20 12:14:49,702 DEBUG [org.springframework.jdbc.core.StatementCreatorUtils] Setting SQL statement parameter value: column index 2, parameter value [N], value class [java.lang.String], SQL type unknown 2011-06-20 12:14:49,705 DEBUG [org.springframework.jdbc.datasource.DataSourceUtils] Returning JDBC Connection to DataSource 2011-06-20 12:14:49,705 ERROR [edu.harvard.i2b2.ontology.dao.ConceptDao] Incorrect result size: expected 1, actual 0
It's searching for a c_table_cd = i2b2 but in i2b2metadata.table_access there is no c_table_cd = i2b2. If I add c_table_cd = i2b2 then the error goes away. Is this a bug somewhere?
Do you know when v1.6 RC4 will be released?
Thanks,
Johnny Phan Programmer Analyst II UTHealth School of Biomedical Informatics 713-500-3939 Dat.Q.Phan.uth.tmcDat.Q.Phan.uth.tmc


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From: Davis, Michael (Oncology) Sent: Monday, June 27, 2011 11:33 AM To: i2b2 AUG Members
Subject: Observation Set No longer returns
I was testing the PDO Analysis Tools in v 1.6 (web client) and noticed it does not return the observation_set anymore in the PDO response, even though this is checked as an option. The events and patients are returned correctly in the response. I used the following from demo data:
<ns2:observation_set panel_name="\\BIRN\BIRN\oasis\Clinical Measures\Clinical Dementia Rating (CDR)\mild dementia\" />
Are there any special permissions needed now to view the observation data? Has anyone else encountered this problem?
Regards,
Mike


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From: John Kilian Sent: Monday, June 27, 2011 9:18 AM To: Nick Holden; Ketty Mobed Cc: i2b2 AUG Members
Subject: distinct codes - need canonical reference
Nick,
You make an excellent case for using a globally accepted reference. Perhaps the WHO utilizes some such standards in its practice.
The data I am charged with loading comes from typical hospital admissions, and uses commonly used demographic parameters in the U.S. clinical setting. Translating from these into an international standard is a simple mapping process, once we know what the international standard is.
Utilizing common standards is key for I2B2 becoming a research tool that spans institutions.
John Kilian, RN, BSCS, BSED
Senior Distributed Applications Programmer/Analyst Hartford Hospital

Holden, Nick 6/26/2011 3:12 AM
Interesting and important work. But can I ask - are these reference demographics specific to the US or global? The latter would obviously be huge, but a US-centric list of ethnicity wouldn't help much in sharing data across the Atlantic.
Nick
Nick Holden
BRU Systems and Database Architect
Leicester Cardiovascular Biomedical Research Unit
Glenfield Hospital

From: Mobed, Ketty Sent: 24 June 2011 21:28 To: John Kilian; Jack London Cc: i2b2 AUG Members
Subject: distinct codes - need canonical reference
Currently I am painstakingly (researching) and developing a complete reference demographics ontology (including detailed race, language, religion, country of birth), as we have felt the need here at UCSF as well. I hope to have it published on NCBO BioPortal within the next 2 months. Hopefully this can be used as standard for querying purposes. This might particularly be useful for public health researchers.
Ketty Mobed, PhD MSPH
Research Analyst / Terminologist ITS - Academic Research Systems
UCSF - Campus Box 0707

From: John Kilian Sent: Friday, June 24, 2011 12:37 PM To: Jack London Cc: i2b2 AUG Members
Subject: distinct codes - need canonical reference
I think the idea of loading concept_cd's for various demographic parameters would be instrumental in effect establishing a constraint on the values allowed in these fields in the Patient_Dimension data.
This constraint could provide the uniformity in expression that would enable querying on these fields across various institutional data sources.
John Kilian, RN, BSCS, BSED
Senior Distributed Applications Programmer/Analyst
Hartford Hospital

Jack London 6/24/2011 3:30 PM
I suggest that for Race the federal (OMB, NIH) categories be used (something like "Black or African American", "White","American Indian or Alaska Native", Asian", etc.). This scheme separates out "Ethnicity" ("Hispanic or Latino","not Hispanic or Latino").
BTW, should there also be a separate "Demographics" i2b2 ontology with concept_cd's for race, ethnicity, gender, etc., which then results in a duplication of this PATIENT_DIMENSION data in the OBSERVATION_FACT table?
Jack
Jack London, Ph.D.
Research Professor Cancer Biology Thomas Jefferson University Director, Informatics Shared Resource Kimmel Cancer Center 808 BLSB, 233 S. 10th St. Philadelphia, PA 19107

On Jun 24, 2011, at 3:22 PM, John Kilian wrote:
I am thinking that it is critical to the mission of I2B2 to allow searches across data from various institutions for us to use the same codes, as mentioned below.
There is a need for a canonical reference for various descriptive fields.
Are there any code sets you know of that we can use when loading our data into I2B2?
John Kilian, RN, BSCS, BSED Senior Distributed Applications Programmer/Analyst Hartford Hospital

Robinett,Joel 6/24/2011 2:05 PM
Hi John,
We use the values supplied by our source system (patient billing) for patient demographics.
The idea of using a canonical reference for these values has great merit, but we obviously haven't started this effort yet.