Re: [gpc-informatics] #114: Milestone 2.7 GPC harmonizes with PCORI CDM V1.0
#114: Milestone 2.7 GPC harmonizes with PCORI CDM V1.0 --+ Reporter: campbell | Owner: campbell Type: task | Status: accepted Priority: major | Milestone: initial-data- Component: data-stds | domains Keywords: PCORI CDM V1, GPC data standards | Resolution: Blocking:| Blocked By: 17, 23, 67, | 120 --+ Comment (by campbell): Changing routing on ticket 114 to copy GPC-DEV Thanks Nathan G! -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/114#comment:18 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #114: Milestone 2.7 GPC harmonizes with PCORI CDM V1.0
#114: Milestone 2.7 GPC harmonizes with PCORI CDM V1.0 --+ Reporter: campbell | Owner: campbell Type: task | Status: accepted Priority: major | Milestone: initial-data- Component: data-stds | domains Keywords: PCORI CDM V1, GPC data standards | Resolution: Blocking:| Blocked By: 17, 23, 67, | 120 --+ Comment (by nathan.wilson): Quick Question. What is the purpose of each test and what are the expected/anticipated results for each test in the Milestone_27_TestSQLv4 document? -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/114#comment:19 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #114: Milestone 2.7 GPC harmonizes with PCORI CDM V1.0
#114: Milestone 2.7 GPC harmonizes with PCORI CDM V1.0 --+ Reporter: campbell | Owner: campbell Type: task | Status: accepted Priority: major | Milestone: initial-data- Component: data-stds | domains Keywords: PCORI CDM V1, GPC data standards | Resolution: Blocking:| Blocked By: 17, 23, 67, | 120 --+ Comment (by nathan.wilson): Attached part I of my comments here: https://informatics.gpcnetwork.org/trac/Project/attachment/ticket/114/Milestone_27_TestSQLv4_nsw_comments_part_i.docx These comments focus mainly on the current selection of LOINC codes which are to be used in the queries. Once I know what the purpose and the expected results are, I will comment on the SQL queries themselves. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/114#comment:20 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
[gpc-informatics] #137: Milestone 2.3 Develop approaches to data standardizaion
#137: Milestone 2.3 Develop approaches to data standardizaion +--- Reporter: campbell | Owner: campbell Type: problem| Status: new Priority: major | Milestone: data-stds-plan Component: data-stds | Keywords: standards, interoperation Blocked By: | Blocking: +--- Milestone 2.3 report draft for submission to PCORI -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/137 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
[gpc-informatics] #143: get sample PopMedNet query
#143: get sample PopMedNet query +--- Reporter: dconnolly | Owner: lv Type: task | Status: new Priority: major | Milestone: popmednet Component: data-stds | Keywords: Blocked By: | Blocking: +--- promoting this item from June 24 discussion (#12) to its own ticket: JimC’s expectation was to manage incoming queries by PopMedNet; need the syntax and content of the queries. Need this to ensure the CDM work will meet needs. BobG has requested a sample query to run through our model. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/143 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #143: get sample PopMedNet query
#143: get sample PopMedNet query ---+ Reporter: dconnolly | Owner: lv Type: task | Status: accepted Priority: major | Milestone: popmednet Component: data-stds | Resolution: Keywords: | Blocked By: Blocking: | ---+ Changes (by lv): * status: new = accepted Comment: Call to discuss this is scheduled for 7/21. Updates to follow. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/143#comment:1 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
[gpc-informatics] #144: ETL Annotated Data Dictionary form required by PCORI
#144: ETL Annotated Data Dictionary form required by PCORI +- Reporter: campbell | Owner: dconnolly Type: task | Status: new Priority: major | Milestone: data-stds-plan Component: data-stds | Keywords: ETL Data Dictionary Blocked By: | Blocking: +- Note to DSSNI from Jenny Ibarra: Attached is the PCORnet Extract, Transform, and Load (ETL) Annotated Data Dictionary. The purpose of this form is to provide a mechanism for PCORnet data partners to communicate information about how they transformed their local data into the PCORnet Common Data Model (CDM) Version 1.0. The information will be used to help the PCORnet Coordinating Center better understand the transformation process, appropriate uses of the PCORnet data, and the comparability of data sources. Please review the instructions found on the Overview tab before proceeding. You may contact the DSSNI Task force at ds...@pcornet.org for questions regarding completion of this form. We would like to identify a contact (organization/site, name, email) at each data source who will be coordinating the ETL process. Please send this contact information to ds...@pcornet.org by August 1. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/144 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #31: data elements for ALS cohort characterization
#31: data elements for ALS cohort characterization -+ Reporter: dconnolly| Owner: dconnolly Type: design-issue | Status: assigned Priority: major| Milestone: data-domains2 Component: data-stds| Resolution: Keywords: als-cohort methods-core | Blocked By: 63 Blocking: | -+ Changes (by dconnolly): * cc: campbell, rwaitman (removed) * cc: gpc-dev@…, tshireman (added) Comment: Replying to [comment:12 dconnolly]: ... I'm not entirely sure that it's entirely free of sensitive details, so I'm not sure how to share it more widely. I made a new folder in the PCORNet Central desktop and put my work there: [https://pcornet.centraldesktop.com/c4gpc/folder/4029536/#folder:4029536 Methods Core Cohort Characterization] Wendy, you might want to share your work there too. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/31#comment:13 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #31: data elements for ALS cohort characterization
#31: data elements for ALS cohort characterization -+ Reporter: dconnolly| Owner: tshireman Type: design-issue | Status: assigned Priority: major| Milestone: data-domains2 Component: data-stds| Resolution: Keywords: als-cohort methods-core | Blocked By: 63 Blocking: | -+ Changes (by dconnolly): * owner: dconnolly = tshireman Comment: Dr. Shireman, In the July 14 MethodsCore call we talked about having you attend the next ALS call to discuss things like what **physical exam** from section 6 of the [wiki:WikiStart#GPCProposal GPC proposal] mean (cf. comment:11). For the call in details, see: - [http://www.mail-archive.com/gpc-als@listserv.kumc.edu/msg00047.html ALS call July 25 11am] Kieran, Russ plans to attend, as well as several others from the DevTeams: Phillip Reeder, Jim !McClay, someone from Wisconsin, Glenn Bushee. I wonder how to get this on the agenda. I'll try you by phone. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/31#comment:14 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
[gpc-informatics] #146: map CDM-in-i2b2 to existing i2b2 data and/or ontologies
#146: map CDM-in-i2b2 to existing i2b2 data and/or ontologies --+-- Reporter: dconnolly| Owner: dconnolly Type: enhancement | Status: new Priority: major| Milestone: initial-data-domains Component: data-stds| Keywords: Blocked By: | Blocking: --+-- splitting the map CDM-in-i2b2 to existing i2b2 data and/or ontologies part out of #109. See especially ticket:109#comment:14 Strategies may vary from site to site. For example: - UNMC can deploy changes to their EMR quickly enough to embed mappings there, so that their i2b2 concept codes are based on standard terms (e.g. LOINC:xyz); so all they have to do is put those concept codes in the `c_basecode` column of the CDM-in-i2b2 metadata rows. - KUMC doesn't expect to deploy mappings in their EMR until later in the project, so their i2b2 concept codes are those codes native to the ERM (e.g. COMPONENT_ID:nnn). These component IDs can be assigned to children of the CDM-in-i2b2 concept paths. In either case, a query that uses the CDM-in-i2b2 terminology will find the relevant patients and data. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/146 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #109: represent PCORI CDM terminology as i2b2 metadata (was: mapping to PCORI CDM (aka mini-sentinel data model))
#109: represent PCORI CDM terminology as i2b2 metadata --+--- Reporter: rwaitman | Owner: dconnolly Type: enhancement | Status: accepted Priority: major | Milestone: initial-data-domains Component: data-sharing | Resolution: Keywords:| Blocked By: 89 Blocking: 145, 146 | --+--- Changes (by dconnolly): * cc: mhoag, ngraham, campbell, hhickman (removed) * cc: gpc-dev@… (added) * blocking: 145 = 145, 146 Comment: reducing scope of this ticket; see #145, #146 for other parts. approximate a popmednet query by an i2b2 query should probably be its own ticket too, but until we have an example query (#143) it's hardly worth the bother. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/109#comment:16 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form required by PCORI
#144: ETL Annotated Data Dictionary form required by PCORI -+- Reporter: campbell | Owner: ngraham Type: task | Status: assigned Priority: major| Milestone: data-stds-plan Component: data-stds| Resolution: Keywords: ETL Data Dictionary | Blocked By: 145 Blocking: | -+- Changes (by dconnolly): * owner: dconnolly = ngraham * status: new = assigned -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/144#comment:3 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form required by PCORI
#144: ETL Annotated Data Dictionary form required by PCORI -+ Reporter: campbell | Owner: ngraham Type: task | Status: assigned Priority: major| Milestone: popmednet Component: data-stds| Resolution: Keywords: ETL Data Dictionary | Blocked By: 145 Blocking: | -+ Changes (by dconnolly): * milestone: data-stds-plan = popmednet Comment: milestone:data-stds-plan (2.3) was submitted July 7. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/144#comment:4 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #145: transform i2b2 query results to PCORNet CDM
#145: transform i2b2 query results to PCORNet CDM --+- Reporter: dconnolly | Owner: dconnolly Type: enhancement | Status: new Priority: major | Milestone: data-stds-plan Component: data-sharing | Resolution: Keywords:| Blocked By: 109 Blocking: 144 | --+- Comment (by dconnolly): milestone:data-stds-plan (2.3) was submitted July 7. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/145#comment:1 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #145: transform i2b2 query results to PCORNet CDM
#145: transform i2b2 query results to PCORNet CDM --+ Reporter: dconnolly | Owner: dconnolly Type: enhancement | Status: new Priority: major | Milestone: popmednet Component: data-sharing | Resolution: Keywords:| Blocked By: 109 Blocking: 144 | --+ Changes (by dconnolly): * milestone: data-stds-plan = popmednet -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/145#comment:2 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #145: transform i2b2 query results to PCORNet CDM
#145: transform i2b2 query results to PCORNet CDM
--+
Reporter: dconnolly | Owner: ngraham
Type: enhancement | Status: assigned
Priority: major | Milestone: popmednet
Component: data-sharing | Resolution:
Keywords:| Blocked By: 109
Blocking: 144 |
--+
Changes (by dconnolly):
* owner: dconnolly = ngraham
* status: new = assigned
Comment:
We can start on this to answer queries for #144; for example, to count
unique DEMOGRAPHICS.PATID:
{{{
with demographics as (
select pd.patient_num patid,
case when bio.concept_cd is not null then 'Y'
else 'N' end biobank_flag
from blueherondata.patient_dimension pd
left join blueherondata.observation_fact bio
on bio.patient_num = pd.patient_num
and bio.concept_cd like 'KUMC|BSR|SAMPLE_DESC:%'
)
select count(distinct d.patid)
from demographics d;
}}}
Not directly related to #144 perhaps, but by way of example of integrating
info from the fact table:
{{{
with demographics as (
select pd.patient_num patid,
case when bio.concept_cd is not null then 'Y'
else 'N' end biobank_flag
from blueherondata.patient_dimension pd
left join blueherondata.observation_fact bio
on bio.patient_num = pd.patient_num
and bio.concept_cd like 'KUMC|BSR|SAMPLE_DESC:%'
)
select count(distinct d.patid)
from demographics d
where biobank_flag = 'Y';
}}}
--
Ticket URL:
http://informatics.gpcnetwork.org/trac/Project/ticket/145#comment:3
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Re: [gpc-informatics] #114: Milestone 2.7 GPC harmonizes with PCORI CDM V1.0
#114: Milestone 2.7 GPC harmonizes with PCORI CDM V1.0 --+ Reporter: campbell | Owner: campbell Type: task | Status: accepted Priority: major | Milestone: initial-data- Component: data-stds | domains Keywords: PCORI CDM V1, GPC data standards | Resolution: Blocking:| Blocked By: 17, 23, 67, | 120 --+ Comment (by campbell): As part of report to PCORI for milestones 2.1, 2.5 and 2.7; it seems logical to me that we consolidate our reporting requirements and simplify procedures for creating aggregate GPC stats. I have enclosed a draft revision of the PCORI form for discussion today Jim -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/114#comment:21 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #146: map CDM-in-i2b2 to existing i2b2 data and/or ontologies
#146: map CDM-in-i2b2 to existing i2b2 data and/or ontologies
-+---
Reporter: dconnolly| Owner: ngraham
Type: enhancement | Status: assigned
Priority: major| Milestone: initial-data-domains
Component: data-stds| Resolution:
Keywords: | Blocked By: 109
Blocking: 144 |
-+---
Comment (by dconnolly):
Nathan, how about moving this decode(...) stuff to the local heron mapping
layer? There's nothing that constrains all GPC sites to use these codes.
{{{
/* Transform i2b2 star schema to CDM (#145). This should work across all
GPC sites.
In fact, it should be shareable with SCHILS too.
*/
...
-- Decode sex - default is 'NI'=No Information
, decode(sex_cd, 'u', 'UN', 'm', 'M', 'f', 'F', '@', 'NI', 'NI') sex
}}}
p.s. I was going to add this as an issue in
[https://bitbucket.org/njgraham/pcori-annotated-data-dictionary/ the code
repo]; what do you think about turning on the issue tracker there?
--
Ticket URL:
http://informatics.gpcnetwork.org/trac/Project/ticket/146#comment:3
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Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form required by PCORI
#144: ETL Annotated Data Dictionary form required by PCORI -+ Reporter: campbell | Owner: ngraham Type: task | Status: assigned Priority: major| Milestone: popmednet Component: data-stds| Resolution: Keywords: ETL Data Dictionary | Blocked By: 145, 146 Blocking: | -+ Comment (by dconnolly): Volunteers from July 29 call (#12) to fill out (at least) the Description tab: - DevTeams#uthscsa : Angela - DevTeams#wisc: Nathan Wilson - DevTeams#mcw: Glenn -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/144#comment:8 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #145: transform i2b2 query results to PCORNet CDM
#145: transform i2b2 query results to PCORNet CDM --+ Reporter: dconnolly | Owner: ngraham Type: enhancement | Status: assigned Priority: major | Milestone: popmednet Component: data-sharing | Resolution: Keywords:| Blocked By: 109 Blocking: 144 | --+ Comment (by ngraham): I believe I've mapped i2b2 - CDM at least enough to answer the Data Summary questions in the PCORnet ETL Annotated Data Dictionary spreadsheet (see ticket:144#comment:14). For performance reasons, I ended up using tables for the CDM objects rather than views. See also [https://bitbucket.org/njgraham/pcori-annotated-data- dictionary/src/d87b6950b4f653b52f93ae9b9a2fe0d4ac972ffa/README.rst?at=default README.rst]. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/145#comment:5 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form required by PCORI
#144: ETL Annotated Data Dictionary form required by PCORI -+--- Reporter: campbell | Owner: ngraham Type: task | Status: assigned Priority: major| Milestone: initial-data-domains Component: data-stds| Resolution: Keywords: ETL Data Dictionary | Blocked By: 145, 146 Blocking: | -+--- Changes (by dconnolly): * milestone: popmednet = initial-data-domains -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/144#comment:15 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #44: portable HERON ETL for NAACCR
#44: portable HERON ETL for NAACCR -+ Reporter: dconnolly| Owner: dconnolly Type: enhancement | Status: assigned Priority: major| Milestone: data-agg1 Component: etl-dev | Resolution: Keywords: | Blocked By: Blocking: 119 | -+ Changes (by dconnolly): * milestone: = data-agg1 -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/44#comment:3 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form required by PCORI
#144: ETL Annotated Data Dictionary form required by PCORI -+--- Reporter: campbell | Owner: ngraham Type: task | Status: assigned Priority: major| Milestone: initial-data-domains Component: data-stds| Resolution: Keywords: ETL Data Dictionary | Blocked By: 145, 146 Blocking: | -+--- Comment (by ngraham): I've uploaded a draft of the [https://pcornet.centraldesktop.com/c4gpc/file/33713907/ ETL Annotated Data Dictionary for KUMC] to the PCORNet central desktop. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/144#comment:17 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #114: Milestone 2.7 GPC harmonizes with PCORI CDM V1.0
#114: Milestone 2.7 GPC harmonizes with PCORI CDM V1.0 --+ Reporter: campbell | Owner: campbell Type: task | Status: accepted Priority: major | Milestone: initial-data- Component: data-stds | domains Keywords: PCORI CDM V1, GPC data standards | Resolution: Blocking:| Blocked By: 17, 23, 67, | 120 --+ Comment (by ngraham): I've created a [https://pcornet.centraldesktop.com/c4gpc/folder/4142694/ folder called PCORI CDM Compliance Worksheet] on the PCORNet Central Desktop and uploaded a [https://pcornet.centraldesktop.com/c4gpc/file/33714066/ draft of the compliance worksheet for KUMC]. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/114#comment:25 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #146: map CDM-in-i2b2 to existing i2b2 data and/or ontologies
#146: map CDM-in-i2b2 to existing i2b2 data and/or ontologies -+--- Reporter: dconnolly| Owner: ngraham Type: enhancement | Status: assigned Priority: major| Milestone: initial-data-domains Component: data-stds| Resolution: Keywords: | Blocked By: 109 Blocking: 144 | -+--- Comment (by ngraham): I've attempted to fill in the rest of the CDM fields from HERON/i2b2 - see [https://bitbucket.org/njgraham/pcori-annotated-data- dictionary/commits/all pcori-annotated-data-dictionary]. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/146#comment:6 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form required by PCORI
#144: ETL Annotated Data Dictionary form required by PCORI -+--- Reporter: campbell | Owner: campbell Type: task | Status: assigned Priority: major| Milestone: initial-data-domains Component: data-stds| Resolution: Keywords: ETL Data Dictionary | Blocked By: 145, 146 Blocking: | -+--- Changes (by ngraham): * owner: ngraham = campbell Comment: Dr. Campbell, [http://listserv.kumc.edu/pipermail/gpc-dev/2014q3/000430.html As I understand it, you are collecting the spreadsheets to submit to PCORI, right?] I'll reassign to you...though that makes you the reporter (customer) and the owner which might not be ideal. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/144#comment:18 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #56: shareable synthetic test data sets: Epic clarity, i2b2, NAACCR, ...
#56: shareable synthetic test data sets: Epic clarity, i2b2, NAACCR, ... --+ Reporter: dconnolly | Owner: bokov Type: enhancement | Status: assigned Priority: major | Milestone: data-quality-plan Component: data-sharing | Resolution: Keywords:| Blocked By: Blocking:| --+ Comment (by dconnolly): I realized last night that the unit tests for the Data Builder (#134 #87) include code to generate a mock i2b2 star schema. It's currently very limited, but I had an idea: Make a spreadsheet with diagnoses, the labs etc. used to diagnose them, and the meds etc. used to treat them (insulin). ||= Condition =||= Indication =||= Treatment =|| || Diabetes||A1C || Insulin|| || Diabetes||BMI || || || MI || Pulse || Aspirin|| || Sepsis || || Antibiotic || And use those as the basis to generate test encounters. Refinements: - value distributions for labs etc. (mean, std dev) - probabilities to go with the relationships - sequences of related encounters: normal results, abnormal, diagnosis, treatment, normal -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/56#comment:15 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #114: Milestone 2.7 GPC harmonizes with PCORI CDM V1.0
#114: Milestone 2.7 GPC harmonizes with PCORI CDM V1.0 --+ Reporter: campbell | Owner: campbell Type: task | Status: accepted Priority: major | Milestone: initial-data- Component: data-stds | domains Keywords: PCORI CDM V1, GPC data standards | Resolution: Blocking:| Blocked By: 17, 23, 67, | 120 --+ Comment (by lv): Marshfield has a draft posted: https://pcornet.centraldesktop.com/c4gpc/file/33747295/ -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/114#comment:26 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #31: data elements for ALS cohort characterization
#31: data elements for ALS cohort characterization -+ Reporter: dconnolly| Owner: jhe Type: design-issue | Status: assigned Priority: major| Milestone: data-agg1 Component: data-stds| Resolution: Keywords: als-cohort methods-core | Blocked By: 63 Blocking: | -+ Changes (by dconnolly): * cc: gchen2@… (added) -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/31#comment:19 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form required by PCORI
#144: ETL Annotated Data Dictionary form required by PCORI -+--- Reporter: campbell | Owner: campbell Type: task | Status: assigned Priority: major| Milestone: initial-data-domains Component: data-stds| Resolution: Keywords: ETL Data Dictionary | Blocked By: 145, 146 Blocking: | -+--- Comment (by gbushee): Uploaded MCW draft of Annotated Data Dictionary with numbers to: https://pcornet.centraldesktop.com/c4gpc/folder/4134009/#folder:4134009 - Glenn -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/144#comment:19 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form required by PCORI
#144: ETL Annotated Data Dictionary form required by PCORI -+--- Reporter: campbell | Owner: campbell Type: task | Status: assigned Priority: major| Milestone: initial-data-domains Component: data-stds| Resolution: Keywords: ETL Data Dictionary | Blocked By: 145, 146 Blocking: | -+--- Comment (by nateapathy): I've uploaded my draft of the [https://pcornet.centraldesktop.com/c4gpc/file/33770797/ CMH ETL Annotated Data Dictionary] to the PCORNet Central Desktop -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/144#comment:22 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #109: represent PCORI CDM terminology as i2b2 metadata
#109: represent PCORI CDM terminology as i2b2 metadata --+--- Reporter: rwaitman | Owner: ngraham Type: enhancement | Status: assigned Priority: major | Milestone: initial-data-domains Component: data-sharing | Resolution: Keywords:| Blocked By: 89 Blocking: 145, 146 | --+--- Changes (by dconnolly): * owner: dconnolly = ngraham * status: accepted = assigned Comment: Nathan and I started loading the SCILHS stuff (Version 1.4 - 8/19/14) in hopes of double-checking that we're in sync, but we didn't finish. Nathan, over to you; let me know when you've done the next bit. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/109#comment:19 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #155: Define Encounter
#155: Define Encounter --+- Reporter: lv| Owner: campbell Type: design-issue | Status: new Priority: major | Milestone: data-stds-gov-plan Component: data-stds | Resolution: Keywords:| Blocked By: Blocking:| --+- Changes (by dconnolly): * cc: gpc-dev (removed) * cc: gpc-dev@… (added) Comment: This looks like #120; how is it different? -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/155#comment:1 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #157: CMD 2.x review: outpatient medication dispense etc.
#157: CMD 2.x review: outpatient medication dispense etc. ---+ Reporter: dconnolly | Owner: huhickman Type: task | Status: assigned Priority: major | Milestone: Component: data-stds | Resolution: Keywords: | Blocked By: Blocking: | ---+ Changes (by dconnolly): * cc: ngraham, jcampbell (removed) * cc: gpc-dev@… (added) * owner: dconnolly = huhickman * status: new = assigned Comment: Hubert, would you please go over the notes of our discussion with Jim C. and re-assign this to him? ref: - [http://listserv.kumc.edu/pipermail/gpc-dev/2014q3/000517.html gpc-dev 23 Sep meeting notes for review] -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/157#comment:1 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form required by PCORI
#144: ETL Annotated Data Dictionary form required by PCORI -+--- Reporter: campbell | Owner: campbell Type: task | Status: closed Priority: major| Milestone: initial-data-domains Component: data-stds| Resolution: fixed Keywords: ETL Data Dictionary | Blocked By: Blocking: | -+--- Changes (by campbell): * status: assigned = closed * resolution: = fixed Comment: PCORI accepted our ETL ADDS Singing off Jim -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/144#comment:24 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #157: CDM 2.x review: outpatient medication dispense etc. (was: CMD 2.x review: outpatient medication dispense etc.)
#157: CDM 2.x review: outpatient medication dispense etc. ---+ Reporter: dconnolly | Owner: jcampbell Type: task | Status: assigned Priority: major | Milestone: Component: data-stds | Resolution: Keywords: | Blocked By: Blocking: | ---+ -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/157#comment:4 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #155: Define Encounter type terms and Epic ETL (was: Define Encounter)
#155: Define Encounter type terms and Epic ETL --+- Reporter: lv| Owner: campbell Type: design-issue | Status: reopened Priority: major | Milestone: data-stds-gov-plan Component: data-stds | Resolution: Keywords:| Blocked By: Blocking: 160 | --+- Changes (by dconnolly): * status: closed = reopened * resolution: invalid = * blocking: = 160 Old description: Create a GPC definition for Encounter; may be based upon input from DSSNI or unique to the network. Discussed on the dev call 9/16/14. New description: Create a GPC definition for Encounter; may be based upon input from DSSNI or unique to the network. - SQL queries to classify Epic CLARITY encounters according to type - ''Cattails, Cerner design should follow straightforwardly'' - term hierarchy (names, paths) for - aggregated counts on babel - federated queries initially discussed on the dev call 9/16/14. -- Comment: Looks like next step could be to get details on this: Epic has provided an unfortunate excess of encounters such that administrative, billing and non-patient care events are all assigned as encounters. Segregating between ED and hospitalizations as well as ambulatory surgery is a bit convoluted but we have sorted out the Clarity data structures necessary to do so. - [http://listserv.kumc.edu/pipermail/gpc-dev/2014q3/000373.html Campbell 15 Aug] -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/155#comment:3 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #84: governance policies for data standardization (PMO milestone 2.1) (was: governance policies for standardizing data)
#84: governance policies for data standardization (PMO milestone 2.1) -+- Reporter: campbell | Owner: campbell Type: enhancement | Status: closed Priority: major| Milestone: data-stds-gov-plan Component: data-stds| Resolution: fixed Keywords: | Blocked By: Blocking: | -+- Changes (by dconnolly): * cc: ngraham (removed) * cc: gpc-dev@… (added) * status: assigned = closed * resolution: = fixed Comment: This issue seems to be addressed by the relevant sections of: - **GPC Milestone Deliverable 2.X_SOP.docx** \\Jim Campbell Sep 30, 2014 6:52 AM \\[http://listserv.kumc.edu/pipermail/gpc-dev/2014q3/000554.html fwd by Dan C.] -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/84#comment:4 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #114: Milestone 2.7 GPC harmonizes with PCORI CDM V1.0
#114: Milestone 2.7 GPC harmonizes with PCORI CDM V1.0 --+ Reporter: campbell | Owner: campbell Type: task | Status: accepted Priority: major | Milestone: initial-data- Component: data-stds | domains Keywords: PCORI CDM V1, GPC data standards | Resolution: Blocking:| Blocked By: 23 --+ Changes (by dconnolly): * blockedby: 17, 23, 67, 120 = 23 Comment: we addressed enough of #17, #67, #120 for this work -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/114#comment:29 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #109: represent PCORI CDM terminology as i2b2 metadata
#109: represent PCORI CDM terminology as i2b2 metadata --+ Reporter: rwaitman | Owner: dconnolly Type: enhancement | Status: assigned Priority: major | Milestone: data-domains2 Component: data-sharing | Resolution: Keywords:| Blocked By: 89 Blocking: 145, 146 | --+ Changes (by dconnolly): * owner: ngraham = dconnolly -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/109#comment:20 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #31: data elements for ALS cohort characterization
#31: data elements for ALS cohort characterization -+ Reporter: dconnolly| Owner: jhe Type: design-issue | Status: assigned Priority: major| Milestone: data-agg1 Component: data-stds| Resolution: Keywords: als-cohort methods-core | Blocked By: 63 Blocking: | -+ Comment (by jhe): Drs Jeffrey Statland, John Chen, Scott Koertner, and Wendy He had a meeting this afternoon, discussing the progress of the ALS cohort characterization and future steps. Jeff gave a lot insignts on what would be interesting information for this patient population. He will come up with a list of prioritized variables for data query. Besides demographics, stand of care will be the focus of the list. Some trivial notes Demographic variables (of particular interest): occupation (employed or not) Livng situation (along or live with others, marital status) (found this variable in Heron but not many patients have the information) Economic status (may come from insurance information) Standar of care Medication (Only one FDA approved medication for ALS, but there are many medicaitons for specific symptoms, such as drooling, muscle spasm. Device: bipap Found ALSFRS in flowsheet and Pba (pseudo bulbar) score. Jeff will find out when the clinic started using these scales. Others Jeff thougt that the 1900+ ALS cases in Heron is more than expected. (more than half of them are dead though. But the 800 alive ones are also more than expected based on the patients seen in the clinic) John mentioned that a patient need to have at least 2 ALS outpatient encounters be be qualified as a ALS patients (this may reduce the patient volumn) Jeff mentioned that it is important to find out what happended to patients before they were diagnozed with ALS (This is regarded as research question that we can work on later) Although there is no specific diagnosis date for ALS in Heron. It would be interesting to show the distribition of the time difference between first ALS encounter and time of death. The expected median is 3 years. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/31#comment:20 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #158: usable view of LOINC lab terms
#158: usable view of LOINC lab terms -+ Reporter: rwaitman | Owner: budh0007 Type: enhancement | Status: assigned Priority: major| Milestone: data-domains2 Component: data-stds| Resolution: Keywords: | Blocked By: Blocking: 68 | -+ Changes (by dconnolly): * milestone: = data-domains2 -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/158#comment:3 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #31: data elements for ALS cohort characterization
#31: data elements for ALS cohort characterization -+ Reporter: dconnolly| Owner: jhe Type: design-issue | Status: assigned Priority: major| Milestone: data-agg1 Component: data-stds| Resolution: Keywords: als-cohort methods-core | Blocked By: 63 Blocking: | -+ Comment (by dconnolly): Replying to [comment:21 jhe]: [...] 2.Jeff mentioned that there is “problem list” in O2 that is easier for identifying comorbidities. Are they in Heron? If yes, where they are? Yes, the problem list is a collection of modifiers in the Diagnosis Hierarchy: - Problem status - Active - Deleted - Resolved p.s. thanks for the notes; more on meds separately -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/31#comment:23 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #31: data elements for ALS cohort characterization
#31: data elements for ALS cohort characterization -+ Reporter: dconnolly| Owner: jhe Type: design-issue | Status: assigned Priority: major| Milestone: data-agg1 Component: data-stds| Resolution: Keywords: als-cohort methods-core | Blocked By: 63 Blocking: | -+ Comment (by ngraham): Replying to [comment:21 jhe]: 1.Do medications in Heron include physician’s prescription data or they are KU pharmacy’s fulfilling prescriptions data? If the clinician orders the medication in Epic/O2, it should be in HERON. I'm not sure if this is the same as the prescription workflow or not. If you query based on medication(s) in HERON (without specifying a modifier) you should be including patients who ever had an order recorded in the Epic system for the selected medication(s) whether or not a dispense was recorded. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/31#comment:24 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
[gpc-informatics] #178: determine whether last.visit is the last fulfilled visit or the last scheduled visit
#178: determine whether last.visit is the last fulfilled visit or the last scheduled visit +--- Reporter: mish | Owner: dconnolly Type: problem| Status: new Priority: major | Milestone: data-quality2 Component: data-stds | Keywords: Blocked By: | Blocking: +--- Dan, [...] Is there a way finding out whether last.visit is the last fulfilled visit or the last scheduled visit? I think it is important for research purpose. If it is the last real visits with potential entry errors, then it is a quality issue. If it is the scheduled last visit that may not be fulfilled, then it is a validity issue as we may no use it to calculate survival time depending on % of last scheduled visits unfulfilled. Thanks, Wendy -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/178 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #87: Deploy, document R Data Builder demo service
#87: Deploy, document R Data Builder demo service --+ Reporter: dconnolly | Owner: dconnolly Type: task | Status: accepted Priority: major | Milestone: data-agg1 Component: data-sharing | Resolution: Keywords:| Blocked By: 134 Blocking: 119 | --+ Comment (by dconnolly): What a pain... after a big hassle getting the python Oracle drivers installed, it turns out the i2b2 1.7 VM uses postgres. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/87#comment:44 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #87: Deploy, document R Data Builder demo service
#87: Deploy, document R Data Builder demo service --+ Reporter: dconnolly | Owner: dconnolly Type: task | Status: accepted Priority: major | Milestone: data-agg1 Component: data-sharing | Resolution: Keywords:| Blocked By: 134 Blocking: 119 | --+ Comment (by gkowalski): Tee hee ... -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/87#comment:45 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #178: determine whether last.visit is the last fulfilled visit or the last scheduled visit
#178: determine whether last.visit is the last fulfilled visit or the last scheduled visit ---+ Reporter: mish | Owner: hhickman Type: problem| Status: assigned Priority: major | Milestone: data-quality2 Component: data-stds | Resolution: Keywords: | Blocked By: Blocking: | ---+ Changes (by dconnolly): * owner: dconnolly = hhickman * status: new = assigned Comment: Hubert, How are you determining visit type from Epic clarity data? Would you please share your SQL code? (or point me/us to it, if you already have) -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/178#comment:1 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #157: CDM 2.x review: outpatient medication dispense etc.
#157: CDM 2.x review: outpatient medication dispense etc. ---+ Reporter: dconnolly | Owner: lv Type: task | Status: assigned Priority: major | Milestone: data-domains2 Component: data-stds | Resolution: Keywords: | Blocked By: Blocking: | ---+ Changes (by dconnolly): * owner: jcampbell = lv * priority: minor = major * milestone: = data-domains2 Comment: So we have [http://listserv.kumc.edu/pipermail/gpc-dev/2014q4/000638.html a new CDM 2.x draft]. Is it responsive to the concerns we discussed 23 Sep (comment:1)? Laurel, would you either - review the draft and let us know, or - find a volunteer or two to do so in or before the Nov 21 meeting? -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/157#comment:6 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #157: CDM 2.x review: outpatient medication dispense etc.
#157: CDM 2.x review: outpatient medication dispense etc. ---+ Reporter: dconnolly | Owner: preeder Type: task | Status: assigned Priority: major | Milestone: data-domains2 Component: data-stds | Resolution: Keywords: | Blocked By: Blocking: | ---+ Changes (by dconnolly): * owner: lv = preeder Comment: Phillip, Between Jim C.'s holiday and the fact that he wasn't with us on the Sep 23 call, I'm not sure whether our concerns were relayed to the DSSNI TF. Do you have a handy way to check? Maybe it doesn't much matter, but it would be nice to know whether they have already considered this input. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/157#comment:8 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
[gpc-informatics] #182: Complete LOINC standardization of CDM V1 and share metadata with GPC
#182: Complete LOINC standardization of CDM V1 and share metadata with GPC -+- Reporter: campbell| Owner: hickman Type: | Status: new enhancement| Milestone: morning-star Priority: major | Keywords: Data standardization, common data Component: data-stds | model Blocked By: | Blocking: -+- Shortly after I left for vacation, I received response from Regenstrief with the additional LOINC codes that were needed for standardization of CDM V1. I have attached a spreadsheet with LOINC coding for CDM V1. Hubert and Mike will deploy the rest of the metadata at Nebraska and issue a shared copy on Babel for all GPC members to employ. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/182 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #87: Deploy, document R Data Builder demo service
#87: Deploy, document R Data Builder demo service --+ Reporter: dconnolly | Owner: dconnolly Type: task | Status: accepted Priority: major | Milestone: data-agg1 Component: data-sharing | Resolution: Keywords:| Blocked By: 134, 179 Blocking: 119 | --+ Comment (by dconnolly): I automated much of the installation/deployment as `i2b2_vm_deploy.mk` in [dc5bc82ee900/heron_extract]. BuilderSaga is much shorter as a result; you might give it a try. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/87#comment:47 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #158: usable view of LOINC lab terms
#158: usable view of LOINC lab terms -+ Reporter: rwaitman | Owner: budh0007 Type: enhancement | Status: assigned Priority: major| Milestone: data-domains2 Component: data-stds| Resolution: Keywords: | Blocked By: Blocking: 68 | -+ Comment (by nateapathy): Lucky for us, Lori already did some of this in January. Unfortunately, the LOINC file is ~460MB so I won't be uploading/attaching it here. Here's the link to the site specifically for the Bioportal-to-i2b2 translations: http://i2b2.bioontology.org/ And here's the link to the Bioportal API tool: https://community.i2b2.org/wiki/display/NCBO/NCBO+Ontology+Tools -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/158#comment:10 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #182: Complete LOINC standardization of CDM V1 and share metadata with GPC
#182: Complete LOINC standardization of CDM V1 and share metadata with GPC -+- Reporter: campbell | Owner: huhickman Type: enhancement | Status: assigned Priority: major| Milestone: morning- Component: data-stds| star Keywords: Data standardization, common data| Resolution: model | Blocked By: Blocking: 23, 109 | -+- Changes (by dconnolly): * owner: hickman = huhickman * status: new = assigned -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/182#comment:3 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #109: represent PCORI CDM terminology as i2b2 metadata
#109: represent PCORI CDM terminology as i2b2 metadata --+ Reporter: rwaitman | Owner: dconnolly Type: enhancement | Status: accepted Priority: major | Milestone: data-domains2 Component: data-sharing | Resolution: Keywords:| Blocked By: 89, 182 Blocking: 145, 146 | --+ Comment (by dconnolly): I managed to scrape the CDM 2.x spec today [https://bitbucket.org/DanC/pcornet- dm/commits/b14948170b242fa5c6e9c9d9b1b834ed8022ac33 b14948170b24/pcornet- dm] It's not quite in the form that I need for generating i2b2 metadata, so I haven't merged this `cdm2x` branch. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/109#comment:24 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #87: Deploy, document R Data Builder demo service
#87: Deploy, document R Data Builder demo service --+ Reporter: dconnolly | Owner: dconnolly Type: task | Status: accepted Priority: major | Milestone: data-agg1 Component: data-sharing | Resolution: Keywords:| Blocked By: 134, 179 Blocking: 119 | --+ Comment (by gkowalski): Well I got to step 5 and received the error ( See ScreenShot_11_4_install_fail.png attachment ) . I can connect to it from my native OS with pgadmin3 tool so the database is running correctly. I'm connecting as user postgres -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/87#comment:50 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #87: Deploy, document R Data Builder demo service
#87: Deploy, document R Data Builder demo service
--+
Reporter: dconnolly | Owner: dconnolly
Type: task | Status: accepted
Priority: major | Milestone: data-agg1
Component: data-sharing | Resolution:
Keywords:| Blocked By: 134, 179
Blocking: 119 |
--+
Comment (by gkowalski):
My default ./var/lib/pgsql/9.1/data/pg_hba.conf file reads :
{{{
# TYPE DATABASEUSERADDRESS METHOD
hostall all 127.0.0.1/32trust
hostall all 192.0.0.0/32trust
hostall all 0.0.0.0/0 trust
hostall all 141.0.0.0/32trust
hostall all ::1/128 ident
}}}
--
Ticket URL:
http://informatics.gpcnetwork.org/trac/Project/ticket/87#comment:51
gpc-informatics http://informatics.gpcnetwork.org/
Greater Plains Network - Informatics
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Re: [gpc-informatics] #87: Deploy, document R Data Builder demo service
#87: Deploy, document R Data Builder demo service
--+
Reporter: dconnolly | Owner: dconnolly
Type: task | Status: accepted
Priority: major | Milestone: data-agg1
Component: data-sharing | Resolution:
Keywords:| Blocked By: 134, 179
Blocking: 119 |
--+
Comment (by gkowalski):
Past step 5 , had to edit the /var/lib/pgsql/9.1/data/pg_hba.conf to add a
local entry :
{{{
# TYPE DATABASEUSERADDRESS METHOD
local all all trust
hostall all 127.0.0.1/32trust
hostall all 192.0.0.0/32trust
hostall all 0.0.0.0/0 trust
hostall all 141.0.0.0/32trust
hostall all ::1/128 ident
}}}
--
Ticket URL:
http://informatics.gpcnetwork.org/trac/Project/ticket/87#comment:52
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Re: [gpc-informatics] #87: Deploy, document R Data Builder demo service
#87: Deploy, document R Data Builder demo service
--+
Reporter: dconnolly | Owner: dconnolly
Type: task | Status: accepted
Priority: major | Milestone: data-agg1
Component: data-sharing | Resolution:
Keywords:| Blocked By: 134, 179
Blocking: 119 |
--+
Comment (by gkowalski):
Well I rau the query on Endocrine like the demo video showed and it didn't
work. I didn't get the Job queued message , but rather a broken link (
See broken-link.png image attachment ) .
I don't see the JSON file in the queue dir to process :
[root@localhost heron]# ls -l /var/log/data_builder/queue/
total 0
[root@localhost heron]#
Also No errors in the server.log jboss file, just normal stuff :
{{{
14:50:47,494 INFO [edu.harvard.i2b2.crc.dao.OracleDAOFactory]
(Thread-138) Using datasource java:/QueryToolDemoDS
14:50:47,546 INFO [stdout] (Thread-138) panel accuracy scale100
14:50:47,547 INFO
[edu.harvard.i2b2.crc.dao.setfinder.querybuilder.temporal.TemporalPanelConceptItem]
(Thread-138) Item value constrain sql [Ljava.lang.String;@a9cc99
14:50:47,547 INFO [stdout] (Thread-138) insert into QUERY_GLOBAL_TEMP
(patient_num, panel_count)
14:50:47,552 INFO [stdout] (Thread-138) with t as (
14:50:47,553 INFO [stdout] (Thread-138) select f.patient_num
14:50:47,553 INFO [stdout] (Thread-138) from public.observation_fact f
14:50:47,553 INFO [stdout] (Thread-138) where
14:50:47,554 INFO [stdout] (Thread-138) f.concept_cd IN (select
concept_cd from public.concept_dimension where concept_path LIKE
'\\i2b2\\Diagnoses\\Endocrine disorders (240-259)\\%')
14:50:47,554 INFO [stdout] (Thread-138) group by f.patient_num
14:50:47,554 INFO [stdout] (Thread-138) )
14:50:47,555 INFO [stdout] (Thread-138) select t.patient_num, 0 as
panel_count from t
14:50:47,559 INFO [stdout] (Thread-138) *
14:50:47,559 INFO [stdout] (Thread-138) insert into DX ( patient_num
) select * from ( select distinct patient_num from QUERY_GLOBAL_TEMP
where panel_count = 0 ) q
14:50:47,561 INFO [edu.harvard.i2b2.crc.dao.DataSourceLookupHelper]
(Thread-138) Located DataSource for hiveId=[i2b2demo] projectId=[/Demo/]
and ownerId =[@]
14:50:47,562 INFO [edu.harvard.i2b2.crc.dao.OracleDAOFactory]
(Thread-138) Using datasource java:/QueryToolDemoDS
14:50:47,641 INFO [edu.harvard.i2b2.crc.dao.DataSourceLookupHelper]
(Thread-138) Located DataSource for hiveId=[i2b2demo] projectId=[/Demo/]
and ownerId =[@]
14:50
}}}
But when I look in that directory I don't see an output file , not sure
where the timeline_3.db came from but you had one of those also :
[root@localhost heron]# pwd
/home/demo/heron
[root@localhost heron]# ls -ltr
total 128
-rw-r--r-- 1 root root 126976 Nov 4 14:19 timeline_3.db
[root@localhost heron]#
--
Ticket URL:
http://informatics.gpcnetwork.org/trac/Project/ticket/87#comment:53
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Re: [gpc-informatics] #87: Deploy, document R Data Builder demo service
#87: Deploy, document R Data Builder demo service
--+
Reporter: dconnolly | Owner: dconnolly
Type: task | Status: accepted
Priority: major | Milestone: data-agg1
Component: data-sharing | Resolution:
Keywords:| Blocked By: 134, 179
Blocking: 119 |
--+
Comment (by gkowalski):
OK , opened up the dev tools in chrome to see if I could see a better
error on the post
Request is wierd :
http://192.168.116.144/webclient/js-
i2b2/cells/plugins/fsm/KaplanMeierStat/assets/icefish2.gif
Response :
{{{
!DOCTYPE HTML PUBLIC -//IETF//DTD HTML 2.0//EN
htmlhead
title404 Not Found/title
/headbody
h1Not Found/h1
pThe requested URL /webclient/js-
i2b2/cells/plugins/fsm/KaplanMeierStat/assets/icefish2.gif was not found
on this server./p
hr
addressApache/2.2.15 (CentOS) Server at 192.168.116.144 Port
80/address
/body/html
}}}
--
Ticket URL:
http://informatics.gpcnetwork.org/trac/Project/ticket/87#comment:54
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Re: [gpc-informatics] #87: Deploy, document R Data Builder demo service
#87: Deploy, document R Data Builder demo service --+ Reporter: dconnolly | Owner: dconnolly Type: task | Status: accepted Priority: major | Milestone: data-agg1 Component: data-sharing | Resolution: Keywords:| Blocked By: 134, 179 Blocking: 119 | --+ Comment (by dconnolly): Replying to [comment:52 gkowalski]: Past step 5 , had to edit the /var/lib/pgsql/9.1/data/pg_hba.conf to add a local entry Strange! I wonder why I didn't have to do that. You'd think that we were running **exactly** the same bits. You're definitely running i2b2vmware-1703a.zip Version: 1.7.03a? -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/87#comment:55 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #87: Deploy, document R Data Builder demo service
#87: Deploy, document R Data Builder demo service --+ Reporter: dconnolly | Owner: dconnolly Type: task | Status: accepted Priority: major | Milestone: data-agg1 Component: data-sharing | Resolution: Keywords:| Blocked By: 134, 179 Blocking: 119 | --+ Comment (by dconnolly): Replying to [comment:54 gkowalski]: ... assets/icefish2.gif ... title404 Not Found/title That shouldn't matter. You can put some image there if you like, but the lack of it shouldn't stop anything from working. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/87#comment:56 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #87: Deploy, document R Data Builder demo service
#87: Deploy, document R Data Builder demo service --+ Reporter: dconnolly | Owner: dconnolly Type: task | Status: accepted Priority: major | Milestone: data-agg1 Component: data-sharing | Resolution: Keywords:| Blocked By: 134, 179 Blocking: 119 | --+ Comment (by gkowalski): Replying to [comment:55 dconnolly]: Replying to [comment:52 gkowalski]: Past step 5 , had to edit the /var/lib/pgsql/9.1/data/pg_hba.conf to add a local entry Strange! I wonder why I didn't have to do that. You'd think that we were running **exactly** the same bits. You're definitely running i2b2vmware-1703a.zip Version: 1.7.03a? Yes , only difference is I'm running it on my Mac as the native OS and using VMWare Fusion . I didn't have to install a second Network adapter , the first was able to get to the internet and download the required packages. Sure I'm using the same heron_extract.zip that you used ? I assume so . I may try a fresh install again , this time with the pg_hba.conf mod first before the installation . -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/87#comment:57 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #87: Deploy, document R Data Builder demo service
#87: Deploy, document R Data Builder demo service --+ Reporter: dconnolly | Owner: dconnolly Type: task | Status: accepted Priority: major | Milestone: data-agg1 Component: data-sharing | Resolution: Keywords:| Blocked By: 134, 179 Blocking: 119 | --+ Comment (by gkowalski): Really webclient.d.ts ? not webclient.d.js ? -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/87#comment:59 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #87: Deploy, document R Data Builder demo service
#87: Deploy, document R Data Builder demo service --+ Reporter: dconnolly | Owner: dconnolly Type: task | Status: accepted Priority: major | Milestone: data-agg1 Component: data-sharing | Resolution: Keywords:| Blocked By: 134, 179 Blocking: 119 | --+ Comment (by dconnolly): Replying to [comment:58 gkowalski]: Hmmm . Missing the entire KaplanMeierStat directory : `KaplanMeierStat` was never really relevant to this data builder stuff; it's is a separate project now. See ticket:134#comment:5 -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/87#comment:60 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #87: Deploy, document R Data Builder demo service
#87: Deploy, document R Data Builder demo service --+ Reporter: dconnolly | Owner: dconnolly Type: task | Status: accepted Priority: major | Milestone: data-agg1 Component: data-sharing | Resolution: Keywords:| Blocked By: 134, 179 Blocking: 119 | --+ Comment (by dconnolly): Replying to [comment:59 gkowalski]: Really webclient.d.ts ? not webclient.d.js ? part of an exploration into [http://www.typescriptlang.org/ typescript]. Probably dead code now. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/87#comment:61 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #87: Deploy, document R Data Builder demo service
#87: Deploy, document R Data Builder demo service --+ Reporter: dconnolly | Owner: dconnolly Type: task | Status: accepted Priority: major | Milestone: data-agg1 Component: data-sharing | Resolution: Keywords:| Blocked By: 134, 179 Blocking: 119 | --+ Comment (by gkowalski): Got it , Removed the line : exports.animation_addr = ( js- i2b2/cells/plugins/fsm/KaplanMeierStat/assets/icefish2.gif); from /var/www/html/webclient/js- i2b2/cells/plugins/fsm/DFBuilder/tool_widgets_orig.js and it worked . -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/87#comment:62 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #87: Deploy, document R Data Builder demo service
#87: Deploy, document R Data Builder demo service
--+
Reporter: dconnolly | Owner: dconnolly
Type: task | Status: accepted
Priority: major | Milestone: data-agg1
Component: data-sharing | Resolution:
Keywords:| Blocked By: 134, 179
Blocking: 119 |
--+
Comment (by gkowalski):
Next Step failed :
{{{
[root@localhost deploy]# make -f i2b2_vm_deploy.mk
request1=/var/log/data_builder/queue/2014-11-04T16\:39\:25.443684-demo.json
i2b2_vm_deploy.mk:100: *** target pattern contains no `%'. Stop.
[root@localhost deploy]# cat
/var/log/data_builder/queue/2014-11-04T16\:39\:25.443684-demo.json
{username: demo, filename: endotest, label: Endocrine
disor@13:50:45 [11-4-2014] [demo] [PATIENTSET_5], patient_set: 5,
concepts: {keys: [i2b2_DIAG\\i2b2\\Diagnoses\\Endocrine disorders
(240-259)\\], names: [Endocrine disorders]}}[root@localhost deploy]#
}}}
--
Ticket URL:
http://informatics.gpcnetwork.org/trac/Project/ticket/87#comment:63
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Re: [gpc-informatics] #87: Deploy, document R Data Builder demo service
#87: Deploy, document R Data Builder demo service
--+
Reporter: dconnolly | Owner: dconnolly
Type: task | Status: accepted
Priority: major | Milestone: data-agg1
Component: data-sharing | Resolution:
Keywords:| Blocked By: 134, 179
Blocking: 119 |
--+
Comment (by gkowalski):
From the Video :
{{{
[root@localhost cdr2edc]# python dfbuilder.py
/usr/local/heron_extract/deploy/test.conf
/var/log/data_builder/2014-11-04T16\:39\:25.412647-demo.json
Traceback (most recent call last):
File dfbuilder.py, line 939, in module
_trusted_main()
File dfbuilder.py, line 937, in _trusted_main
gethostname=socket.gethostname)
File dfbuilder.py, line 859, in main
username = params['username']
KeyError: 'username'
[root@localhost cdr2edc]#
}}}
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[gpc-informatics] #191: represent PCORI CDM 2.x terminology as i2b2 metadata
#191: represent PCORI CDM 2.x terminology as i2b2 metadata ---+-- Reporter: dconnolly | Owner: dconnolly Type: design-issue | Status: new Priority: minor | Milestone: morning-star Component: data-stds | Keywords: Blocked By: 109 | Blocking: ---+-- separating 2.x work out to reduce scope of #109 -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/191 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #145: transform (ETL) GPC i2b2 data to PCORNet CDM (was: transform i2b2 query results to PCORNet CDM)
#145: transform (ETL) GPC i2b2 data to PCORNet CDM --+ Reporter: dconnolly | Owner: ngraham Type: enhancement | Status: assigned Priority: major | Milestone: data-domains2 Component: data-sharing | Resolution: Keywords:| Blocked By: 109 Blocking: 160 | --+ Comment (by ngraham): Dan and I decided on a new summary - see comment:9 We're not really converting i2b2 query results, either; so the ticket summary should change. I'm not inspired with a better summary just now, though. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/145#comment:12 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #31: data elements for ALS cohort characterization
#31: data elements for ALS cohort characterization -+ Reporter: dconnolly| Owner: jhe Type: design-issue | Status: assigned Priority: major| Milestone: data-agg1 Component: data-stds| Resolution: Keywords: als-cohort methods-core | Blocked By: 63 Blocking: | -+ Changes (by jhe): * cc: skoertner@… (added) -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/31#comment:25 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
[gpc-informatics] Batch modify: #68, #102, #120, #157, #158, #103, #77, #155
Batch modification to #68, #102, #120, #157, #158, #103, #77, #155 by dconnolly: milestone to data-domains3 Comment: reducing scope of milestone:data-domain2 to priority datatypes -- Tickets URL: http://informatics.gpcnetwork.org/trac/Project/query?id=68%2C102%2C120%2C157%2C158%2C103%2C77%2C155 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #186: Querying age by numerical constraints
#186: Querying age by numerical constraints -+ Reporter: huhickman| Owner: huhickman Type: problem | Status: closed Priority: major| Milestone: data-domains2 Component: data-stds| Resolution: fixed Keywords: age valueset obesity-cohort | Blocked By: Blocking: | -+ Changes (by dconnolly): * cc: gpc-dev@… (added) * keywords: age valueset = age valueset obesity-cohort * status: new = closed * resolution: = fixed Comment: UNMC's recent babel update (ticket:64#comment:26) includes the relevant details in the Age Range term under UNMC: Demographics. I'm closing this to put it on the group agenda. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/186#comment:1 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #186: Querying age by numerical constraints
#186: Querying age by numerical constraints -+ Reporter: huhickman| Owner: huhickman Type: problem | Status: closed Priority: major| Milestone: data-domains2 Component: data-stds| Resolution: fixed Keywords: age valueset obesity-cohort | Blocked By: Blocking: | -+ Comment (by dconnolly): Hubert, the terms you delivered has both Age and Age at Visit in the usual buckets-of-years style as in the i2b2 demo metadata, but it has only Age term with this scalar range style. Did you leave out scalar Age at Visit on purpose? -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/186#comment:2 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #157: CDM 2.x review: outpatient medication dispense etc.
#157: CDM 2.x review: outpatient medication dispense etc. ---+ Reporter: dconnolly | Owner: rwaitman Type: task | Status: assigned Priority: major | Milestone: data-domains3 Component: data-stds | Resolution: Keywords: | Blocked By: Blocking: | ---+ Changes (by dconnolly): * cc: gpc-dev@… (removed) * cc: rwaitman, preeder, campbell (added) * owner: preeder = rwaitman Comment: Replying to [comment:8 dconnolly]: ... I'm not sure whether our concerns were relayed to the DSSNI TF. I gather Russ has taken this up with the PCORNet steering committee. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/157#comment:11 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #178: determine whether last.visit is the last fulfilled visit or the last scheduled visit
#178: determine whether last.visit is the last fulfilled visit or the last scheduled visit ---+ Reporter: mish | Owner: huhickman Type: problem| Status: assigned Priority: major | Milestone: data-quality2 Component: data-stds | Resolution: Keywords: | Blocked By: 155 Blocking: | ---+ Changes (by dconnolly): * blockedby: = 155 Comment: In reviewing the details from Keith W. ... - [http://listserv.kumc.edu/pipermail/gpc-dev/2014q4/000723.html Oct 28] - [http://listserv.kumc.edu/pipermail/gpc-dev/2014q4/000741.html Nov 3] with SQL query I realize that determining encounter type ETL is actually #155. I expect the answer to this derives naturally from that design. Or in other words: this is a use case for that design. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/178#comment:5 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #178: determine whether last.visit is the last fulfilled visit or the last scheduled visit
#178: determine whether last.visit is the last fulfilled visit or the last scheduled visit ---+ Reporter: mish | Owner: huhickman Type: problem| Status: assigned Priority: major | Milestone: data-quality2 Component: data-stds | Resolution: Keywords: | Blocked By: 155 Blocking: | ---+ Comment (by huhickman): Note that our research Clarity instance at UNMC is in SQL Server and our i2b2 databases are in Oracle. This particular view lives in SQL Server because of how we have to divide our work up - our Oracle Dynamic Gateway for SQL Server has habit of toppling over on queries that are complicated so some of our processing is done in SQL Server. This is one example of that. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/178#comment:6 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #178: determine whether last.visit is the last fulfilled visit or the last scheduled visit
#178: determine whether last.visit is the last fulfilled visit or the last scheduled visit ---+ Reporter: mish | Owner: huhickman Type: problem| Status: assigned Priority: major | Milestone: data-quality2 Component: data-stds | Resolution: Keywords: | Blocked By: 155 Blocking: | ---+ Comment (by campbell): Wendy Encounters are rolled out unequally across GPC right now. Given differences in system installations, I suggest you consider the PCORI common data model for encounters which we all must implement (and are implementing or have implemented. Encounter types indicate whether encounters are scheduled or completed: ENCOUNTR TYPE (LOINC: 75525-6) COMPLETED: AV=AMBULATORY VISIT; ED=EMERGENCY DEPARTMENT; IS= NONINSTITUTIONAL INPATIENT STAY; IP=INPATIENT STAY; OA=OTHER AMBULATORY VISIT SCHEDULED OR ADMINISTRATIVE: OT=OTHER; UN=UNKNOWN; NI=NO INFORMATION Our source data at UNMC has considerable more detail regarding administrative types of encounters and you should tell us if you have needs for tracking those types of events. The Completed encounter types are actual face-to-face encounters of some type with the patient and are those you presumably what you want for research. The others are administrative or scheduling encounters and should be ignored for patient care issues Have I answered your question? Jim Campbell -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/178#comment:7 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #155: Define Encounter type terms and Epic ETL
#155: Define Encounter type terms and Epic ETL --+ Reporter: lv| Owner: huhickman Type: design-issue | Status: assigned Priority: major | Milestone: data-domains3 Component: data-stds | Resolution: Keywords:| Blocked By: Blocking: 160, 178 | --+ Changes (by dconnolly): * owner: campbell = huhickman * status: reopened = assigned Comment: Hubert, Thanks for sharing the details of UNMC's approach to encounter types (attachment:pcori_encounters.sql:ticket:178 and ticket:178#comment:6). It's reasonably clear how that query lets you compute PCORNet CDM summary stats on encounter type. But we still have to decide what encounter terms GPC will use. The UNMC metadata on babel (as of Nov 6 ticket:64#comment:26) doesn't seem to include the results under UNMC: Encounters. Do you plan to continue working in that direction? -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/155#comment:7 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #178: determine whether last.visit is the last fulfilled visit or the last scheduled visit
#178: determine whether last.visit is the last fulfilled visit or the last scheduled visit ---+ Reporter: mish | Owner: jhe Type: problem| Status: assigned Priority: major | Milestone: data-quality2 Component: data-stds | Resolution: Keywords: | Blocked By: 155 Blocking: | ---+ Comment (by jhe): Replying to [comment:7 campbell]: Jim, Thanks for the clarification. There is a variable called last.visit among the demographic variables in Heron. What we wanted to find out is whether last.visit is a fulfilled visit or not. If yes, then we know the patient was last known alive on that day. if no, then we can't use last.visit as last known alive date. It is great to know that encounter type can differentiate encounters completered and others. But this is not enough for answering the original question. When we run a query, we pull encounters related to a specific disease only, so the last encounter of the patient with the hospital (likely related other diseases) may not be in the pulled data. I don't know whether the date of last.visit corresponds to the last encounter (among all encounters with the hospitals). If it is, then we need to find that encounter and its type (completed or not). Dan and Tamara: do you know whether we can do this? If last.visit is not linked to an encounter in the system, then we are back to the begining ot the original question: is last.visit fulfilled or scheduled only. Thanks, Wendy Wendy Encounters are rolled out unequally across GPC right now. Given differences in system installations, I suggest you consider the PCORI common data model for encounters which we all must implement (and are implementing or have implemented. Encounter types indicate whether encounters are scheduled or completed: - ENCOUNTR TYPE (LOINC: 75525-6) - COMPLETED: AV=AMBULATORY VISIT; ED=EMERGENCY DEPARTMENT; IS= NONINSTITUTIONAL INPATIENT STAY; IP=INPATIENT STAY; OA=OTHER AMBULATORY VISIT - SCHEDULED OR ADMINISTRATIVE: OT=OTHER; UN=UNKNOWN; NI=NO INFORMATION Our source data at UNMC has considerable more detail regarding administrative types of encounters and you should tell us if you have needs for tracking those types of events. The Completed encounter types are actual face-to-face encounters of some type with the patient and are those you presumably what you want for research. The others are administrative or scheduling encounters and should be ignored for patient care issues Have I answered your question? Jim Campbell -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/178#comment:9 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #90: Diagnoses Modifiers for data attribution
#90: Diagnoses Modifiers for data attribution --+ Reporter: campbell | Owner: lv Type: design-issue | Status: assigned Priority: major | Milestone: data-domains2 Component: data-stds | Resolution: Keywords:| Blocked By: Blocking: 70, 91, 120 | --+ Changes (by dconnolly): * cc: gpc-dev@… (removed) * cc: gpc-dev@… (added) -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/90#comment:9 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #87: Deploy, document R Data Builder demo service
#87: Deploy, document R Data Builder demo service --+ Reporter: dconnolly | Owner: gkowalski Type: task | Status: assigned Priority: major | Milestone: data-agg1 Component: data-sharing | Resolution: Keywords:| Blocked By: 134, 179 Blocking: 119 | --+ Changes (by dconnolly): * owner: dconnolly = gkowalski * status: accepted = assigned Comment: The screenshare demo went well today. I talked through the BuilderSaga#QuickStart screencast, pausing to address questions and issues. - George @ MCW was able to follow along and get it working; whatever problems he saw earlier didn't show up today. - Angela @ UTHSCSA had various issues that should be addressed by starting from a clean i2b2 VM - Phillip and company @ UTSW emerged pretty confident they could get it working, though they weren't quite in sync today. - Keith @ WISC joined a little late and didn't follow step-by-step but seemed confident he could manage. After the basic data builder install, we continued beyond the GPC requirements into the [comment:16 SEINE] technique for delivering data via REDCap. The new portable sqlite3 architecture doesn't provide this functionality yet; we plan to finish it in the upcoming monthly HERON release. So Dan and Nathan demonstrated the current R-based production workflow at KUMC. George has the ball to provide whatever revisions to BuilderSaga seem worthwhile for documentation. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/87#comment:66 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #178: determine whether last.visit is the last fulfilled visit or the last scheduled visit
#178: determine whether last.visit is the last fulfilled visit or the last scheduled visit -+--- Reporter: mish | Owner: dconnolly Type: enhancement | Status: assigned Priority: major| Milestone: cohort-char1 Component: data-stds| Resolution: Keywords: | Blocked By: 155 Blocking: | -+--- Changes (by dconnolly): * owner: jhe = dconnolly * type: problem = enhancement * milestone: data-quality2 = cohort-char1 Comment: Replying to [comment:9 jhe]: ... then we need to find that encounter and its type (completed or not). Dan and Tamara: do you know whether we can do this? Not yet. I expect we will be able to as a consequence of work Nathan is doing on #145 (and perhaps some other internal HERON work). I think Jim's diagnosis and suggested direction makes sense, so I'm changing this from a problem ticket to an enhancement request ad moving it to milestone:cohort-char1. We'll keep you posted on progress, Wendy. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/178#comment:10 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #87: Deploy, document R Data Builder demo service
#87: Deploy, document R Data Builder demo service --+ Reporter: dconnolly | Owner: gkowalski Type: task | Status: assigned Priority: major | Milestone: data-agg1 Component: data-sharing | Resolution: Keywords:| Blocked By: 134, 179 Blocking: 119 | --+ Comment (by dconnolly): George and everybody, I just updated BuilderSaga based on the screenshare demo. The material after BuilderSaga#QuickStart is organized roughly the same way the targets `i2b2_vm_deploy.mk` are, since those targets are known to result in a working system. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/87#comment:67 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #90: Diagnoses Modifiers for data attribution
#90: Diagnoses Modifiers for data attribution --+ Reporter: campbell | Owner: lv Type: design-issue | Status: accepted Priority: major | Milestone: data-domains2 Component: data-stds | Resolution: Keywords:| Blocked By: Blocking: 70, 91, 120 | --+ Changes (by lv): * status: assigned = accepted Comment: Are there are requests from researchers at other sites to use these alternative types of diagnoses? MCRF use our main Diagnosis Table for the majority of our research. Only in a rare case would we go after anything else. Notes: 1. Primary vs. Principle: after a quick, non-comprehensive check, Cattails uses Primary. 2. Primary, Secondary: Currently we pull all diagnoses, without regard for position. To fill Primary and Secondary, we'd need to adjust our ETL. How would other diagnoses be handled? Are only two being loaded per encounter for other sites? 3. Billing Diagnosis: Admit Diagnosis Principle, Admit Diagnosis Secondary, Discharge Diagnosis Principle, Discharge Diagnosis Secondary, Discharge Diagnosis Present on Admis.. - Do these modifiers only apply to inpatient diagnoses? What does Billing mean for Epic? Is this what would be sent on an insurance claim? We could fill some diagnoses for this categories from hospital or insurance plan sources. It would take work. 4. Encounter Diagnosis: Admit Encounter Diagnosis, Discharge Encounter Diagnosis, Primary Encounter Diagnosis, Secondary Encounter Diagnosis, Medical History Diagnosis - How does HSP_ADMIT_DIAGNOSIS differ from HSP_ACCT_ADMIT_DX? I'm not sure how to differentiate between the first two modifiers in this category and the Billing category above. This would be the majority of our diagnoses, as clinical (outpatient). We would need to adjust our ETL as mentioned in item 2 above. On a quick search, only .77% of our diagnoses include the History of type. 5. Order Diagnoses: Order Medication Diagnosis, Order Procedure Diagnosis - Cattails does not link diagnoses to medications. We couldn't accurately fill this. There also isn't a direct association between a procedure and diagnosis. We could do some work to try to fill this, but we'd have to make a lot of assumptions. 6. Problem List Diagnosis: Active Problem, Deleted Problem, Resolved Problem - What does Deleted mean? Entered in error? What does this add for a researcher? The Cattails Problem List table includes Problem Status, Inactive Date, Last Problem Instance, etc. We don't get any requests to pull diagnoses from the Problem List. It would take time to investigate how to integrate this source. 7. Professional Diagnosis: Primary Professional Diagnosis, Secondary Professional Diagnosis - Are these also hospital-related codes? I don't know what ARPB means from the Clarity Table. It would take significant effort for MCRF to accurately implement this series of modifiers. I'd like to hear feedback that the additional elements add value for researchers, as we do not have a local use case. Let me know if this makes sense or if you would like additional clarification. Thanks, Laurel From: Phillip Reeder [phillip.ree...@utsouthwestern.edu] Sent: Wednesday, November 12, 2014 2:13 PM To: gpc-dev@listserv.kumc.edu; campb...@unmc.edu; Dan Connolly Cc: gpc-...@listserv.kuc.edu Subject: Re: [gpc-informatics] #90: Diagnoses Modifiers for data attribution Based on the emails I found, and what is on babel, this is what I think the modifiers should be. The only difference from Babel is in the Billing Diagnosis modifiers where I tried apply what was in the various emails. Cerner had Inactive and Canceled modifiers for the Problem List Diagnosis in one of the emails. I¹m unsure if they need to be added or if they could be mapped to the three modifiers from Epic. For consistency, is there a preference for Principle vs Primary? Does it make a difference? ModifierModifier Code Clarity Table Billing Diagnosis Admit Diagnosis Principle DX|BILL:ADMIT PRINCIPLE HSP_ACCT_ADMIT_DX Admit Diagnosis Secondary DX|BILL:ADMIT SECONDARY HSP_ACCT_ADMIT_DX Discharge Diagnosis Principle DX|BILL:PRINCIPAL HSP_ACCT_DX_LIST Discharge Diagnosis Secondary DX|BILL:SECONDARY HSP_ACCT_DX_LIST Discharge Diagnosis Present on Admis.. DX|BILL:POA HSP_ACCT_DX_LIST Encounter Diagnosis Admit Encounter Diagnosis DX|ENC:ADMIT HSP_ADMIT_DIAGNOSIS Discharge Encounter Diagnosis DX|ENC:DISCHARGE HSP_DISCH_DIAGNOSIS Primary Encounter Diagnosis DX|ENC:PRIMARY PAT_ENC_DX Secondary Encounter Diagnosis DX|ENC:SECONDARY PAT_ENC_DX
Re: [gpc-informatics] #90: Diagnoses Modifiers for data attribution
#90: Diagnoses Modifiers for data attribution --+ Reporter: campbell | Owner: dconnolly Type: design-issue | Status: accepted Priority: major | Milestone: data-domains2 Component: data-stds | Resolution: Keywords:| Blocked By: Blocking: 70, 91, 120 | --+ Comment (by lv): Thanks for this clarification; taking another look, we can use the Diagnosis Sub Type IDS field here. 0 *Not Available 1 Primary 2 Secondary 3 Procedure Scheduled 4 Procedure Incid 5 Procedure RT SRG 6 Complication 8 Other 9 Unspecified Replying to [comment:12 dconnolly]: 2. Primary, Secondary: Currently we pull all diagnoses, without regard for position. To fill Primary and Secondary, we'd need to adjust our ETL. How would other diagnoses be handled? Are only two being loaded per encounter for other sites? I think Secondary is a bit of a misnomer; I think it just means not primary, and there can be may of them. The database column is just a Y/N for primary. It would take significant effort for MCRF to accurately implement this series of modifiers. I'd like to hear feedback that the additional elements add value for researchers, as we do not have a local use case. It seems reasonable to me that if your system doesn't distinguish primary from secondary, you should just report the more general term, e.g. Billing Diagnosis. Or if you don't even know that much, just don't add a modifier at all. For studies that require the distinction, MCRF would have to evaluate the benefit of participating against the cost of adjusting your ETL. But I think I should escalate this issue, as it bears on DataRepositoryManagement, which is included in the GPC data sharing agreement by reference. Am I missing where we would differentiate a source of insurance? Structure seems like it would match Encounter Diagnoses. Could be good to define now, if the goal is to incorporate health plans in the future. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/90#comment:14 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #71: portable HERON ETL for Epic
#71: portable HERON ETL for Epic -+--- Reporter: dconnolly| Owner: bos Type: enhancement | Status: assigned Priority: major| Milestone: Component: etl-dev | Resolution: Keywords: | Blocked By: 127 Blocking: | -+--- Comment (by dconnolly): Angela and company, I see you merged Oct 22 default (28fe7567932b) into your a branch you're working on. Nice! Is the branch you merged into, `UTHSCSA_med_map_curation`, likely to land on your main branch soon? -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/71#comment:11 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #90: Diagnoses Modifiers for data attribution
#90: Diagnoses Modifiers for data attribution --+ Reporter: campbell | Owner: nateapathy Type: design-issue | Status: assigned Priority: major | Milestone: data-domains2 Component: data-stds | Resolution: Keywords:| Blocked By: Blocking: 70, 91, 120 | --+ Changes (by dconnolly): * owner: dconnolly = nateapathy * status: accepted = assigned Comment: JRC writes: I think that Cerner was researching their problem list installation at the time of the Hackathon and we should add their modifiers to problem diagnoses but I would ask Nate Apathy if ?Cerner:Cancelled=Epic:Deleted? or are there differences in meaning between Cerner and Epic on that issue of an erroneous entry that was backed out? -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/90#comment:15 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #90: Diagnoses Modifiers for data attribution
#90: Diagnoses Modifiers for data attribution --+ Reporter: campbell | Owner: nateapathy Type: design-issue | Status: assigned Priority: major | Milestone: data-domains2 Component: data-stds | Resolution: Keywords:| Blocked By: Blocking: 70, 91, 120 | --+ Comment (by nateapathy): That's correct - in the Cerner Millennium Problem List the valid statuses are Active, Cancelled, and Resolved, and Cancelled would be used for the use case you are describing re: Deleted from Epic. We keep the Problems List and Diagnoses List separate (you can turn problems into diagnoses in the chart, of course, but on the database side there are distinct and separate tables (PROBLEM and DIAGNOSIS). For modifiers on diagnosis codes, we only specify between primary and non- primary, as Laurel described earlier in this thread, so I wouldn't vote for Secondary as the modifier of choice. We are using Primary and non- Primary in our current i2b2 projects. It's not reflected in Babel yet because we haven't finished the deployment but I'll have an updated diagnosis ontology in December. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/90#comment:16 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #90: Diagnoses Modifiers for data attribution
#90: Diagnoses Modifiers for data attribution --+ Reporter: campbell | Owner: nateapathy Type: design-issue | Status: assigned Priority: major | Milestone: data-domains2 Component: data-stds | Resolution: Keywords:| Blocked By: Blocking: 70, 91, 120 | --+ Comment (by nateapathy): Replying to [comment:11 dconnolly]: Replying to [comment:10 lv]: Are there are requests from researchers at other sites to use these alternative types of diagnoses? My experience with HERON at KUMC includes at least one researcher who said something like you can't distinguish primary billing diagnosis? Never mind then. Call me when you can. So when i2b2 1.6 came a long with modifiers, we enhanced HERON to use modifiers to make the distinction in our Sep 2012 release: - [https://informatics.kumc.edu/work/blog/heron-waconda-update HERON Waconda update introduces new searching modifiers for Medications and Diagnosis] The CDM spec says Please do not include diagnoses generated from problem lists, which are a different workflow and data-generating activity. HERON at KUMC includes problem list diagnoses, so using a modifier is a straightforward way to filter them out for CDM purposes. We've also heard this same request on the Cerner side, but the meaningful research distinction has always been with Primary vs. Non- Primary and no further granularity has been brought to my attention thus far. Regarding problem list diagnoses, do you mean problems that have been deemed diagnosis-worthy and therefore are only those diagnoses that originated from the problem list? If that's the case, I know that the workflow exists in Cerner to capture that, but I will have to do some more digging to find out how we capture that in our extracts and how it might be brought in to i2b2. Currently we do not have that flag in i2b2, if it is for diagnoses that originated on the problem list. The alternative would be records on the problem list that are coded with diagnosis codes, which on the clinical side don't make them diagnoses, but could cause confusion on this topic. I'll add other comments to separate topics as well. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/90#comment:17 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #90: Diagnoses Modifiers for data attribution
#90: Diagnoses Modifiers for data attribution --+ Reporter: campbell | Owner: nateapathy Type: design-issue | Status: assigned Priority: major | Milestone: data-domains2 Component: data-stds | Resolution: Keywords:| Blocked By: Blocking: 70, 91, 120 | --+ Comment (by nateapathy): Replying to [comment:10 lv]: 3. Billing Diagnosis: Admit Diagnosis Principle, Admit Diagnosis Secondary, Discharge Diagnosis Principle, Discharge Diagnosis Secondary, Discharge Diagnosis Present on Admis.. - Do these modifiers only apply to inpatient diagnoses? What does Billing mean for Epic? Is this what would be sent on an insurance claim? We could fill some diagnoses for this categories from hospital or insurance plan sources. It would take work. CMH is currently working on setting up their billing system feed into the i2b2 database, which will distinguish source of diagnosis (EMR vs. Billing). This will include primary and non-primary as discussed above, as well as a Present on Admit flag. We don't distinguish admit vs. discharge diagnosis in the billing feed data, since it is based on the UB04 and CMS1500 standards that don't specify admit/discharge diagnoses. 4. Encounter Diagnosis: Admit Encounter Diagnosis, Discharge Encounter Diagnosis, Primary Encounter Diagnosis, Secondary Encounter Diagnosis, Medical History Diagnosis - How does HSP_ADMIT_DIAGNOSIS differ from HSP_ACCT_ADMIT_DX? I'm not sure how to differentiate between the first two modifiers in this category and the Billing category above. This would be the majority of our diagnoses, as clinical (outpatient). We would need to adjust our ETL as mentioned in item 2 above. On a quick search, only .77% of our diagnoses include the History of type. I'm also not clear how encounter diagnoses are distinguished. All diagnoses are associated in Cerner at the encounter level, and we do not have a distinction of historical diagnoses in the i2b2 database. We would need to do some work to incorporate this into our ETL as well, if it exists in our extracts. 5. Order Diagnoses: Order Medication Diagnosis, Order Procedure Diagnosis - Cattails does not link diagnoses to medications. We couldn't accurately fill this. There also isn't a direct association between a procedure and diagnosis. We could do some work to try to fill this, but we'd have to make a lot of assumptions. I echo this - we do not link orders to diagnoses either. Is this intended to record medical necessity checking or ABNs? i.e. this is the diagnosis that justifies this medication or procedure? 6. Problem List Diagnosis: Active Problem, Deleted Problem, Resolved Problem - What does Deleted mean? Entered in error? What does this add for a researcher? The Cattails Problem List table includes Problem Status, Inactive Date, Last Problem Instance, etc. We don't get any requests to pull diagnoses from the Problem List. It would take time to investigate how to integrate this source. Per my comment above: Is this problems that were once problems and have been promoted to official diagnoses, or is it entries on the problem list documented with diagnosis codes? It appears from Laurel's comments that it's the latter, which makes sense to me and would be the most straightforward to fulfill. 7. Professional Diagnosis: Primary Professional Diagnosis, Secondary Professional Diagnosis - Are these also hospital-related codes? I don't know what ARPB means from the Clarity Table. +1; I'm not sure how this is different from billing diagnoses. It would take significant effort for MCRF to accurately implement this series of modifiers. I'd like to hear feedback that the additional elements add value for researchers, as we do not have a local use case. This level of granularity would also take a significant amount of effort on the Cerner/CMH side to implement this proposed structure of modifiers. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/90#comment:18 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #71: portable HERON ETL for Epic
#71: portable HERON ETL for Epic -+--- Reporter: dconnolly| Owner: bos Type: enhancement | Status: assigned Priority: major| Milestone: Component: etl-dev | Resolution: Keywords: | Blocked By: 127 Blocking: | -+--- Comment (by bos): Yes, there is no reason not to merge them, but I've got to resolve my merge with ancestor issue. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/71#comment:12 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #186: Querying age by numerical constraints
#186: Querying age by numerical constraints -+ Reporter: huhickman| Owner: jdale Type: problem | Status: assigned Priority: major| Milestone: data-domains2 Component: data-stds| Resolution: Keywords: age valueset obesity-cohort | Blocked By: Blocking: 67 | -+ Changes (by dconnolly): * owner: huhickman = jdale * status: reopened = assigned Comment: Justin volunteered 11 Nov (notes: #12) to try to reproduce Hubert's work. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/186#comment:6 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #31: data elements for ALS cohort characterization
#31: data elements for ALS cohort characterization -+ Reporter: dconnolly| Owner: jhe Type: design-issue | Status: assigned Priority: major| Milestone: data-agg1 Component: data-stds| Resolution: Keywords: als-cohort methods-core | Blocked By: 63 Blocking: | -+ Comment (by jhe): Due to travel and other meetings, John, Jeff, Scott, and Wendy finally met all together on 21st (Scott and Wendy met on Nov 7, Scott, Wendy, and John met on Nov 14). The major issue for ALS cohort characterization is to identify variables needed. We went through a list Jeff made in October but many of them do not identify enough records. At the meeting, we decoded to use ICD9 code to identify variables for comobidities. John provided a list of ICD9 codes for creating charlson comobidity code and Jeff will find ICD 9 codes for other variables. Identifing medications remains an issue. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/31#comment:26 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #31: data elements for ALS cohort characterization
#31: data elements for ALS cohort characterization -+ Reporter: dconnolly| Owner: jhe Type: design-issue | Status: assigned Priority: major| Milestone: data-agg1 Component: data-stds| Resolution: Keywords: als-cohort methods-core | Blocked By: 63 Blocking: | -+ Comment (by jhe): Replying to [comment:23 dconnolly]: We found the problem list under diagnosesclinical(O2 EMR), but there seems to have no content in it. Replying to [comment:21 jhe]: [...] 2. Jeff mentioned that there is “problem list” in O2 that is easier for identifying comorbidities. Are they in Heron? If yes, where they are? Yes, the problem list is a collection of modifiers in the Diagnosis Hierarchy: - Problem status - Active - Deleted - Resolved p.s. thanks for the notes; more on meds separately -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/31#comment:27 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
[gpc-informatics] #198: Epic spring Research Advisory Council Presentation
#198: Epic spring Research Advisory Council Presentation +--- Reporter: campbell | Owner: dconnolly Type: task | Status: new Priority: minor | Milestone: Component: data-stds | Keywords: Blocked By: | Blocking: +--- I am preparing a presentation for submission to the Epic spring research council and am asking if Russ or any members of GPC-DEV are interested in co-presenting? See attached abstract Research council is March 16-18 Jim -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/198 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #87: Deploy, document R Data Builder demo service
#87: Deploy, document R Data Builder demo service --+--- Reporter: dconnolly | Owner: gkowalski Type: task | Status: assigned Priority: major | Milestone: bc-survey-cohort-def Component: data-sharing | Resolution: Keywords:| Blocked By: 134, 179 Blocking: 119 | --+--- Changes (by dconnolly): * milestone: data-agg1 = bc-survey-cohort-def Comment: Plans for the breast cancer survey (KeyGoalTracking#bc-survey) are in flux, and in some versions, deploying the data builder at each site is critical path. So conservatively, I'm moving this to that milestone. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/87#comment:68 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #56: shareable synthetic test data sets: Epic clarity, i2b2, NAACCR, ...
#56: shareable synthetic test data sets: Epic clarity, i2b2, NAACCR, ... --+ Reporter: dconnolly | Owner: dconnolly Type: enhancement | Status: assigned Priority: minor | Milestone: data-domains2 Component: data-sharing | Resolution: Keywords:| Blocked By: Blocking:| --+ Changes (by dconnolly): * owner: bokov = dconnolly * priority: major = minor Comment: So this would be very useful, but it's not blocking progress on any of the more urgent tasks. Can we give this a lower priority? -- [http://listserv.kumc.edu/pipermail/gpc-dev/2014q4/000588.html Alex 6 Oct] Meanwhile, I should share what I did for testing the data builder (#87). -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/56#comment:21 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #158: usable view of LOINC lab terms
#158: usable view of LOINC lab terms -+ Reporter: rwaitman | Owner: budh0007 Type: enhancement | Status: assigned Priority: major| Milestone: data-domains3 Component: data-stds| Resolution: Keywords: | Blocked By: Blocking: 68 | -+ Comment (by jmcclay): Comments from Scott Campbell at UNMC I have created a hierarchical view of the Lab LOINC items for approximately 2000 of the 2500 terms used at UNMC. This also includes orderable codes (i.e. batteries) and performable codes (tests/results). The hierarchy is based on LOINC class and refined by UNMC departments and logical groupings. Note: we have generalized the UNMC departments into categories that should make sense to most medical centers. Jim Campbell is reviewing my categories to ensure that they are in-line with a clinician’s perspective. Based on Jim’s feedback, I will refine and issue a testable code set to Hubert. -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/158#comment:13 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
