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.

Joel Robinett

From: John Kilian Sent: Friday, June 24, 2011 12:08 PM To: Robinett,Joel Cc: Jeff Mather
Subject: distinct codes
Joel,
I am doing an analysis of the distinct codes in the PATIENT_DIMENSION table, and I was wondering if UCHC had more/different codes than I am finding in the DemoData. Are there any I2B2 standards on these fields that you know of? It is critical to querying across datasets for us to share a common nomenclature.
LANGUAGE_CD
english
spanish
german
MARITAL_STATUS_CD
single
married
widow
divorced
RELIGION_CD
christian
jewish
atheist
roman
catholic
muslim
agnostic
RACE_CD
asian
indian
black
white
hispanic
SEX_CD
M
F
SOURCESYSTEM_CD
DEMO
VITAL_STATUS_CD
Y
N
John Kilian, RN, BSCS, BSED
Senior Distributed Applications Programmer/Analyst
Hartford Hospital


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From: Phillips, Lori C. Sent: Thursday, June 23, 2011 11:05 AM To: i2b2 AUG Members
Subject: FW: Invalid between clause error
Forwarding solution to AUG members...
From: Davis, Michael (Oncology) Sent: Thursday, June 23, 2011 10:08 AM To: Phillips, Lori C.
Subject: Invalid between clause error
Lori,
I looked at some of the other LOINC concepts that came with the demo data and noticed that the C_COLUMNDATATYPE for these that executed the BETWEEN correctly were set to 'T' (text), but in my custom concept it was set to 'N' (numeric) C_COLUMNDATATYPE ='N'. I modified the concept to have the Column Data Type set to 'T' and this resolved my issue. I'm not sure what the column data type ='N' is used for but I now understand what my issue was.
Regards,
Mike

From: Phillips, Lori C. Sent: Wednesday, June 22, 2011 3:07 PM To: Davis, Michael (Oncology)
Subject: Invalid between clause error
just curious... Where/how did you fix this?

From: Davis, Michael (Oncology) Sent: Wednesday, June 22, 2011 3:02 PM To: i2b2 AUG Members
Subject: Invalid between clause error
I'm not sure if this was reported by anyone, but I upgraded to use v1.6 code and was able to now see the resulting query in QT_QUERY_MASTER for the between value query. It seems that it is formatting the concept_path statement in the WHERE clause incorrectly for custom (those added to CUSTOM_META table) added concepts. If you look at the SQL below you will noticed that there are missing single quotes around the concept_path LIKE ... statement, which is causing an ORA-00911: invalid character. When I fix this, then my between value works just fine.
select patient_num ,1 from ( select /*+ index(observation_fact fact_cnpt_pat_enct_idx) */ patient_num from i2b2demodata.observation_fact where concept_cd IN (select concept_cd from i2b2demodata.concept_dimension where concept_path LIKE \Custom Metadata\MyTest\Breslow Thickness) AND ( valtype_cd = 'N' AND nval_num BETWEEN 0 and 0.99 AND tval_char ='E' )
group by patient_num having count >= 1 );
Hope this can be corrected in next patch release.
Thanks,
Mike

From: Davis, Michael (Oncology) Sent: Friday, June 17, 2011 3:56 PM To: i2b2 AUG Members
Subject: Invalid between clause error
I set up a numeric value field concept (see c_metadataxml below) and I'm trying to use between value, but after I put in the values (e.g, 0.0 - .99) I get the following error on console:
15:32:24,698 ERROR [ExecRunnable] Invalid between clause [0 and 0.99]edu.harvard.i2b2.common.exception.I2B2DAOException: Invalid between clause [0 and 0.99] edu.harvard.i2b2.common.exception.I2B2DAOException: Invalid between clause [0 and 0.99]edu.harvard.i2b2.common.exception.I2B2DAOException: Invalid between clause [0 and 0.99]
at edu.harvard.i2b2.crc.dao.setfinder.querybuilder.QueryToolUtil.generateSQL(Unknow n Source)
at edu.harvard.i2b2.crc.dao.setfinder.QueryRequestSpringDao.buildSql(Unknown Source)
at edu.harvard.i2b2.crc.dao.setfinder.QueryExecutorDao.executeSQL(Unknown Source)
from c_metadataxml
\Custom Metadata\MyTest\Breslow Thickness\
<?xml version="1.0" encoding="UTF-8"?>
<ValueMetadata>
<Version>3.2</Version>
<CreationDateTime>2011-05-24T14:20:26.026-04:00</CreationDateTime>
<MaxStringLength/>
<DataType>Float</DataType>
<Loinc>3024-7</Loinc>
<Oktousevalues>Y</Oktousevalues>
<LowofLowValue/>
<HighofLowValue/>
<LowofHighValue/>
<HighofHighValue/>
<LowofToxicValue/>
<HighofToxicValue/>
<UnitValues>
<NormalUnits>mm</NormalUnits>
</UnitValues>
</ValueMetadata>

This was in the request:
<panel>
<panel_number>1</panel_number>
<invert>0</invert>
<total_item_occurrences>1</total_item_occurrences>
<item>
<hlevel>2</hlevel>
<item_name>Breslow Thickness</item_name>
<item_key>\\CUST\Custom Metadata\MyTest\Breslow
Thickness\</item_key>
<tooltip>Custom Metadata \ MyTest \ Breslow
Thickness</tooltip>
<class>ENC</class>
<constrain_by_date> </constrain_by_date>
<item_icon>LA</item_icon>
<item_is_synonym>false</item_is_synonym>
<constrain_by_value>
<value_type>NUMBER</value_type>
<value_unit_of_measure>mm</value_unit_of_measure>
<value_operator>BETWEEN</value_operator>
<value_constraint>0 and 0.99</value_constraint>
</constrain_by_value>
</item>
</panel>

GENERATED_SQL was NULL in the QT_QUERY_MASTER.
Anyone have any clues to why this kind of search didn't work?
Regards,
Mike


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From: Peter Beninato Sent: Wednesday, June 22, 2011 6:30 PM To: Niveditha Thota; i2b2 AUG Members
Subject: ORA-00942 error in i2b2 logs
Not sure if this fixed it, but my thought was that the CRC schema aka "DATA" needed SELECT privs on the ontology i2b2 table to make use of the count column.
So I added a GRANT SELECT on i2b2 to [data_schema_name]
In the ETL process and I think that error went away.

From: Niveditha Thota Sent: Wednesday, June 22, 2011 3:27 PM To: i2b2 AUG Members
Subject: ORA-00942 error in i2b2 logs
Hi,
I notice this error in the server.log of JBoss.
ERROR [edu.harvard.i2b2.crc.dao.CRCDAO] Unable to get Estimated Size: ORA-00942: table or view does not exist
2011-06-22 18:16:58,534 INFO [STDOUT] CONCEPT TABLE
Can anyone explain what is leading to this error and how this effects the application.
Thanks,
Nivi


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From: Audrey Hureau Sent: Wednesday, June 22, 2011 9:14 AM To: Phillips, Lori C. Cc: i2b2 AUG Members
Subject: no patient found with set value
Ok Lori, thank you all your help.
Audrey Hureau

2011/6/22 Phillips, Lori C.
Audrey,
You are confusing two different issues:
The workbench query returns number of patients: 39
select count(distinct patient_num) from observation_fact
where concept_cd = 'LOINC:11279-7'
Your query is for number of observations: 68
select count from observation_fact
where concept_cd = 'LOINC:11279-7'
In other words, some patients have more than one 'LOINC:11279-7' observation.
As for your second problem, text values are the same as enumerated values in this case, so it falls under the known bug.
Hope this helps,
Lori

From: Audrey Hureau Sent: Wednesday, June 22, 2011 8:52 AM To: Phillips, Lori C. Cc: i2b2 AUG Members
Subject: no patient found with set value
Hi,
Actually, I already run the query using the demodata set and it is my problem. I work under Oracle environment with the Workbench v.1.5.2.0002. I tried to run the query about the LOINC code 11279-7 and I found 39 patients. But when I looked into the observation_fact table, I found 68 rows matching this code.
Besides, I tried also with text values, not specially with only enumerated values. Is it a bug too?
Thank you all again.
Audrey Hureau

2011/6/22 Phillips, Lori C.
Hi Audrey,
Can you reproduce the problem by running the same type of query using the demodata set? If so, send us the specifics – database type (e.g. oracle), query you ran , workbench version ...
Thanks
Lori

From: Audrey Hureau Sent: Wednesday, June 22, 2011 8:18 AM To: i2b2 AUG Members
Subject: no patient found with set value
Hello everyone,
I am confused about something.
When I try to run a query using the "set value" feature, there is no patient found. However, there are some patients in the observation_fact table which match with my query.
Besides, when I did not use the "set value" feature, some patients are found. But I noticed that not all of the patients are found. Can someone help me please?
Thank you all.
Audrey Hureau


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From: Murphy, Shawn N. Sent: Wednesday, June 22, 2011 8:36 AM To: Audrey Hureau Cc: i2b2 AUG Members
Subject: no patient found with set value
Hi Audrey,
This is a bug in the 1.5 code that prevents the proper execution of the queries that use enumerated values. There is a fix coming out today I believe with a version of 1.5.4.
Thanks,
Shawn Murphy MD
Communicating with handheld

On Jun 22, 2011, at 8:18 AM, Audrey Hureau wrote:
Hello everyone,
I am confused about something.
When I try to run a query using the "set value" feature, there is no patient found. However, there are some patients in the observation_fact table which match with my query.
Besides, when I did not use the "set value" feature, some patient are found. But I noticed that not all of the patients are found.
Can someone help me please?
Thank you all.
Audrey Hureau


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From: Murphy, Shawn N. Sent: Tuesday, June 21, 2011 9:38 AM To: Russ Waitman; Haijun Qiu; i2b2 AUG Members
Subject: openldap user authentication
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 Sent: Monday, June 06, 2011 4:43 PM To: Haijun Qiu; i2b2 AUG Members
Subject: 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.edu/work/ticket/8
Russ Waitman
Associate Professor Director of Medical Informatics Department of Biostatistics University of Kansas Medical Center

Qiu, Haijun 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


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From: Mendis, Michael E. Sent: Thursday, June 16, 2011 10:49 AM To: Jack London; i2b2 AUG Members members
Subject: obtaining i2b2 version
Jack,
Sorry about the confusion. If you view the source of the webclient (View->View Page Source) on your browser, that should tell you the version of the webclient. The latest released version is 1.5.3, which is listed correctly in the view source. But some earlier 1.5 versions prior to 1.5.3 might be listed as 1.5 even though they are 1.5.1.
Sorry again about the confusion,
mike

On 6/16/11 9:30 AM, Jack London wrote:
How can one get the exact version number (and release) of an instance of the i2b2 web client?
We have two instances of the web client, and clicking "Help" will display "Version 1.5" and "Updated July 15, 2010" for both. But they behave differently in a significant way when you display entries in a query result patient set:
with one, if there are nulls in certain PATIENT_DIMENSION columns, such as SEX_CD or RACE_CD, "undefined" is listed for that column in the patient list, > and the list quickly is displayed, while with the other (an earlier deployment), the web client application "hangs," never returning the patient set list. For this instance, the fix is > to never have nulls in these columns, but rather some string like "Unknown."
We thought we had deployed the same web client application, but obviously there are differences in the code. (Assuming that this is not the result of some configuration setting.)
So how can we get a definitive statement of the application version and release?
thanks,
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


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From: Peter Beninato Sent: Wednesday, June 15, 2011 10:49 AM To: Audrey Hureau; i2b2 AUG Members Cc: Wynden, Rob
Subject: Analysis View questions
Hi,
I think the breakdown on the Analysis comes from the patient_dimension, if your LOAD processes does not populate that information in the table, then that is likely why it does not get charted in the analysis tool.
Regarding export of patient datasets.
What version of I2B2 are you using? I think 1.6 is suppose to support reusing a patient set in a query.
Are you re-running your query or just hoping there is some way to reuse the patient set of the previous query.
Currently, our system is just interested in providing counts, so I don't have much to share in regards to exporting patient sets but, I have seen a utility that UCSF has developed "view creator" which you might be interested. Contact Rob Wynden for more info

Peter Beninato - OCTRI DW Developer
Oregon Health & Science University

From: Audrey Hureau Sent: Wednesday, June 15, 2011 1:37 AM To: i2b2 AUG Members
Subject: Analysis View questions
Hi,
To be more specific, the issus that I explained in the second part in my previous message is about queries which are running on my own data. Indeed, the differents graphic can all be seen on installation data. My problem is really about my own data. Anyone does have a idea? Thank you again.
Audrey Hureau

2011/6/14 Audrey Hureau
Hi everyone,
I have some questions about queries' results.
Is it possible to export the patient list? When I check the patient list in the Analysis Types, I can see the list in the Previous Queries view but I can't get it back. I would like to export it or save it in a document for example. So, I would like to know if there is any way to do do?
Besides, I have some issues about the Graphic Analyses in the Analysis view. When I check some analysis types like the number of patients, the gender patient breakdown and the age patient breakdown and then I run the query, I can visualize the number of patients but I can't see any data on the gender graphic nor the age patient graphic. Do you where this issue comes from?
Thank you all.
Audrey Hureau


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From: Murphy, Shawn N. Sent: Wednesday, June 15, 2011 8:55 AM To: Phillips, Lori C.; Cowall, Jeff; i2b2 AUG Members
Subject: "Find Terms/Search by Name" drop down has no effect in v1.5?
Yes, in 1.6 you can have multiple ontology categories in one table.
Thanks,
Shawn.

From: Phillips, Lori C. Sent: Tuesday, June 14, 2011 11:33 AM To: Cowall, Jeff; i2b2 AUG Members
Subject: "Find Terms/Search by Name" drop down has no effect in v1.5?
Jeff,
Good catch.
Yes a change was made to the 1.6 ONT cell to further restrict the category selection on find by name. As you mention, in 1.5 it associated the category with a table and searched within that table. In 1.6 the category itself is used to limit the search to a specific category in an associated table.
Lori

From: Cowall, Jeff Sent: Tuesday, June 14, 2011 10:12 AM To: i2b2 AUG Members
Subject: "Find Terms/Search by Name" drop down has no effect in v1.5?
We have both 1.6rc and 1.5 instances of i2b2, with slightly different data, and have populated the table_access table in both.
We have just one ontology table, with everything in it, in both.
The table access tables in the 1.6 and 1.5 versions look very similar to each other, with a row for each level 1, and c_table_name the same in each row.
In 1.6, selecting a level 1 concept from the drop down properly constrains the search to that subject, while in 1.5, the drop down has no effect at all.
To me, it looks like 1.5 assumes each row is literally in a separate table, while 1.6 uses both the table name and the dimcode to constrain the term search.
Do I have that right?
Jeff "can't wait to get to 1.6" Cowall
University of Michigan


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From: Jack London Sent: Tuesday, June 14, 2011 2:17 PM To: i2b2 AUG Members members Cc: Mendis, Michael E.
Subject: web client query has no generated sql
web client v1.5 queries never terminate. looking at the qt_query_master table, the request xml looks fine, but there is a null in the generated_sql column.
any suggestions as to what can cause this?
thanks,
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


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From: Jeremy Nix Sent: Monday, June 13, 2011 11:30 AM To: Wei,Xintao Cc: i2b2 AUG Members
Subject: I2B2 with SQL 2008
Xintao,
You will want to make sure you are using a SQL Server 2008 compliant JDBC driver. There are several free options out there. Microsoft has there one one here (http://www.microsoft.com/downloads/en/details.aspx?FamilyID=a737000d-68d0-4531-b65dda0f2a735707&displaylang=en).
JTDS also has a driver here (http://sourceforge.net/projects/jtds/files/jtds/1.2.5/jtds-1.2.5-dist.zip/download).
You'll need to extract the appropriate jar file to JBOSS_HOME/server/default/lib. Be sure to remove or rename the existing JDBC drivers here JBOSS_HOME/server/default/lib/sqljdbc.jar and JBOSS_HOME/server/default/lib/jtds-1.2.2.jar. If you rename the files, be sure to change the file extension (sqljdbc.jar.bak, jtds-1.2.2.jar.bak).
If you chose the JTDS JDBC driver, then you will need to update all of the datasource connection files appropriately. Here's what the *-ds.xml files in the JBOSS_HOME/server/default/deploy directory will look like:
<local-tx-datasource>
<jndi-name>QueryToolDemoDS</jndi-name>
<connection-url> jdbc:jtds:sqlserver://SERVER_HAME:SERVER_PORT/DATABASE_NAME</connectionurl>
<driver-class>net.sourceforge.jtds.jdbc.Driver</driver-class>
<user-name>USERNAME</user-name>
<password>PASSWORD</password>
<idle-timeout-minutes>1</idle-timeout-minutes>
<set-tx-query-timeout>true</set-tx-query-timeout>
<metadata>
<type-mapping>MS SQLSERVER2000</type-mapping>
</metadata>
</local-tx-datasource>
Similarly, all of the Spring ApplicationContext.xml files with datasources would need to be updated. They are located in JBOSS_HOME/server/default/conf/*/*ApplicationContext.xml. Here's an example of the definitions there:
<bean id="CRCDataSourceLookup"class="org.apache.commons.dbcp.BasicDataSource" destroy-method="close">
<property name="driverClassName"value="net.sourceforge.jtds.jdbc.Driver" />
<property name="url"value="jdbc:jtds:sqlserver://SERVER_HAME:SERVER_PORT/DATABASE_NAME" />
<property name="username" value="USERNAME" />
<property name="password" value="PASSWORD" />
</bean>
For simplicity, you may just want to try the Microsoft driver first, as it does not require any changes to the datasource definitions. Then, once that configuration is working, you could try the JTDS driver. Currently we are using the JTDS driver for our 2005/2008 instances without issues.
Jeremy Nix
Senior Application Developer Cincinnati Children's Hospital Medical Center

On 06/13/2011 10:49 AM, Wei,Xintao wrote:
igure SQL 2008 to I2B2 server. D


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From: Wei,Xintao Sent: Monday, June 13, 2011 10:50 AM To: i2b2 AUG Members
Subject: I2B2 with SQL 2008
Hi,
A I2B2 server 1.52 has been installed on Windows server 2008 64bit and SQL server 2005 with Java
1.5 and JBoss 4.2.2.GA. However, I was asked to use SQL server 2008 instead of SQL 2005. I have problems to configure SQL 2008 to I2B2 server. Does anyone have the experience about how to configure SQL 2008 for I2B2 server on Windows server 2008? Would you like to share your hand notes or teach me how to do it?
Thank you!
Xintao


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From: Churchill, Susanne E. Sent: Friday, June 10, 2011 4:04 PM To: i2b2 AUG Members
Subject: Final Call for AUG Meeting/Posters/Etc.
Dear Members,
This is the final call for registration for the AUG Meeting June 28-29 in Boston.
IMPORTANT: IF YOU WILL BE BRINGING A POSTER OR WISH TO STAGE A DEMO (WE WILL SCHEDULE THESE CONCURRENTLY WITH THE POSTER SESSION) PLEASE LET ME KNOW BY JUNE 17 AND IDENTIFY THE GENERAL SUBJECT MATTER SO WE CAN GROUP THESE BY SUBJECT AREAS.
THE CURRENT REGISTRATION ROSTER, INCLUDING THE NLP WORKSHOP, POSTER AND DEMO REGISTRATIONS IS ATTACHED FOR YOUR REFERENCE.
We look forward to seeing you; let me know if you have any questions.
Thanks,
Susanne
Susanne E. Churchill, Ph.D.
Executive Director i2b2/Nat'l Center for Biomedical Computing 77 Avenue Louis Pasteur, Room 255 Boston, MA 02115


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From: Cowall, Jeff Sent: Thursday, June 09, 2011 9:34 AM To: i2b2 AUG Members
Subject: Medical Administratrion Record Ontology?
Has anyone built a Med Administration Record ontology from a vendor-based inpatient system like Cerner or Eclipsys?
Thanks,
Jeff


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From: Mauro Sent: Monday, June 06, 2011 11:07 AM To: davismk; i2b2 AUG Members members Cc: Riccardo Bellazzi; Daniele Segagni
Subject: i2b2 Plugins
Hi Mike, here in Pavia we've already built an ontology-based plugin,i.e. a plug-in that has been developed for a specific project /specific ontology.
The current version of the plugin works only after having pre-definedthe ontology, since the client calls a servlet purposely created.
However, we are now working on a new general-purpose plugin that weestimate to deploy within a couple of weeks.
Regards,
Mauro

2011/6/2 Davis, Michael (Oncology)
Does anyone know if someone has developed an export data or table viewer plugin for the web client?
Regards,
Mike
Michael Davis
Sr. Software Architect
University of Pittsburgh Cancer Institute


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From: Yaorong Ge Sent: Sunday, June 05, 2011 7:46 PM To: Churchill, Susanne E.; i2b2 AUG Members
Subject: Collaboration Opportunity
Susanne,
I am interested in developing a primate data warehouse integrating several sources of data at the Wake Forest Univeristy Primate Center including clinical, subclinical, imaging, diatery, and genetic data. At the next level, I am interested in using SHRINE to integrate the Primate Data Warehouse with the Clinical Research Data Warehouse with the goal to accelerate translation between animal and human models. The focus of clinical questions at WFUPC is in cardiovascular diseases and related risk factors. We will use this focus to be the driving biology project.
Please let me know if this is something of interest to you. Thanks.
Yaorong

From: Churchill, Susanne E. Sent: Friday, June 03, 2011 12:01 PM To: i2b2 AUG Members
Subject: Collaboration Opportunity
The NIH has just resurrected the R21 Program that seeks to promote collaborations with National Centers for Biomedical Computing (of which i2b2 is one such). Depending on your focus (note not all Centers have signed up to fund), this may represent an opportunity to work with us on projects of mutual interest.
Please let us know if you are interested and we'll arrange to discuss.
http://grants.nih.gov/grants/guide/pa-files/PAR-08-183.html


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From: Chan, Wayne Sent: Friday, June 03, 2011 4:34 PM To: i2b2 AUG Members
Subject: i2b2 v1.6RC2 query resulted in ~120 Patients in Patient_set when there doesn't appear to be
any.
I did a quick-and-dirty query over the web client, with group1 = "\Visit Details\Visit type", group2 = "\Visit Details\Length of stay", and it resulted in ~120 Patients in its Patient Set. And then I ran the HOM View Creator 1.1 against that query, which created an empty _Patient view.
Further debugging of the SQL statement, used in that view creation, (which is the following):
select PATIENT_NUM, VITAL_STATUS_CD, BIRTH_DATE, DEATH_DATE, SEX_CD, AGE_IN_YEARS_NUM, LANGUAGE_CD, RACE_CD, MARITAL_STATUS_CD, RELIGION_CD, ZIP_CD, STATECITYZIP_PATH, UPDATE_DATE, DOWNLOAD_DATE, IMPORT_DATE, SOURCESYSTEM_CD, UPLOAD_ID from i2b2demodata.patient_dimension where patient_num in (SELECT distinct patient_num FROM i2b2demodata.observation_fact WHERE concept_cd IN (select concept_cd from i2b2demodata.concept_dimension c where concept_path LIKE '\i2b2\Visit Details\Visit type%')) AND patient_num in (SELECT distinct patient_num FROM i2b2demodata.observation_fact WHERE concept_cd IN (select concept_cd from i2b2demodata.concept_dimension c where concept_path LIKE '\i2b2\Visit Details\Length of stay %'))
showed that the concept_cd's from
select concept_cd from i2b2demodata.concept_dimension c where concept_path LIKE '\i2b2\Visit Details\Length of stay%'
are all numerical (which probably shouldn't have been), which resulted in the result from
(SELECT distinct patient_num FROM i2b2demodata.observation_fact WHERE concept_cd IN (select concept_cd from i2b2demodata.concept_dimension c where concept_path LIKE '\i2b2\Visit Details\Length of stay%'))
To be blank, and therefore the rest of the statement.
I have since ran another query using Ischemic Heart Disease across all age spans, and the resulting _Patient view contains 17, exactly what the i2b2 v1.6RC2 query said its Patient_set should be.
So, the question is, why did the i2b2 v1.6RC2 query with group1 = "\Visit Details\Visit type", group2 = "\Visit Details\Length of stay" resulted in ~120 Patients in its Patient Set?

Thanks.
Wayne


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From: Travis Nagler Sent: Wednesday, June 01, 2011 1:49 PM To: i2b2 AUG Members
Subject: 1.5.2 install
I have been able to move slightly past the problem of getting the login error of not having any i2b2 projects associated with the demo user. It allows me to login, then allows me to choose successfully between Demo or Demo2.
According to the PM install instructions Section 4.1, the next screen is supposed to be
however, what I get is
I have tried different browsers (IE, Firefox, Safari), most all of them the newest browser versions, but I have tried an IE 7 and a Firefox 3.6.12 and 3.6.17 with almost no success. The one successful login that got into the correct Admin screen was done by my sys admin. He said he was able to click around and view things there, that everything worked correctly. But then on his IE and Firefox on the same machine, it didn't work.
Has anyone else had browser issues with 1.5.2? Are there certain browser versions that need to be used? I have looked through the page source code and it refers a lot to "JavaScript:i2b2.CRC.ctrlr.QT.[blah]". I have not installed the CRC cell yet (because the instructions have not said to do that yet), but is this something that needs to happen before this Admin page works? I am trying not to veer off the instructions unless absolutely necessary.
Also, it still does not open correctly in the WorkBench, either.
Thanks,
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