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] #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
gpc-informatics http://informatics.gpcnetwork.org/
Greater Plains Network - Informatics
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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
