Where search use cases call for frequent 'drag and drop' of specific values from a multiple-valued code set (as in ethnicity), we have set up both search nodes with linked coded values but also 'LEAF' searches (which must employ c_dimcode as the standard reference, most often LOINC) by value employing the appropriate METADATAXML for the leaf node in the metadata. We will be glad to demo this at the next GPC-DEV call Jim
James R. Campbell MD [email protected] Office: 402-559-7505 Secretary: 402-559-7299 Pager: 402-888-1230 > On Dec 22, 2014, at 9:03 AM, "GPC Informatics" <[email protected]> wrote: > > #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): > > Using the `c_dimcode` in comment:14 doesn't work well for cases where > there are multiple concepts in the GPC/HERON hierarchy map to a single > concept in the PCORI hierarchy. One example is Hispanic: > ||PCORI path||HERON path > ||\PCORI\DEMOGRAPHIC\HISPANIC\Y\||\i2b2\Demographics\Ethnicity\Hispanic\|| > ||\PCORI\DEMOGRAPHIC\HISPANIC\Y\||\i2b2\Demographics\Ethnicity\Hispanic, > Latino or Spanish Origin\|| > > So, instead of using the `c_dimcode` I plan to insert rows into the > concept dimension that map the PCORI paths to the appropriate concept > codes. I plan to do this by building a mapping between the PCORI paths > and the GPC paths (much like we did in [https://bitbucket.org/njgraham > /pcori-annotated-data- > dictionary/src/1c1c0f980377bbd1adbe839edf84d8de92f5b1de/heron_to_pcori.csv?at=default > heron_to_pcori.csv] for the Annotated data Dictionary). > > I tried this out for diagnosis and was able to run a query for `ICD-9-CM` > in the PCORI hierarchy (item key > `<item_key>\\PCORI_\PCORI\DIAGNOSIS\DX_TYPE\09\</item_key>` against the > small KU test data set and return a patient count: > {{{ > Finished Query: "ICD-9-CM@08:59:10" > [2.4 secs] > Compute Time: 1 secs > Number of patients for "ICD-9-CM@08:59:10" > patient_count: 141 > }}} > > Also, demographics (and, specifically, the Hispanic flag noted above). > {{{ > Finished Query: "HISPANIC@09:01:26" > [1.7 secs] > Compute Time: 1 secs > Number of patients for "HISPANIC@09:01:26" > patient_count: 721 > }}} > > -- > Ticket URL: > <http://informatics.gpcnetwork.org/trac/Project/ticket/145#comment:15> > gpc-informatics <http://informatics.gpcnetwork.org/> > Greater Plains Network - Informatics > _______________________________________________ > Gpc-dev mailing list > [email protected] > http://listserv.kumc.edu/mailman/listinfo/gpc-dev The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender. _______________________________________________ Gpc-dev mailing list [email protected] http://listserv.kumc.edu/mailman/listinfo/gpc-dev
