I appreciate Phillip's view on compromise, but this is pretty fundamental to the employment of the LOINC standard.
I think that the choice of concept path by the i2b2 site manager (and the instantiation of the Clinical LOINC ontology in this case) is not a necessary attribute even if a choice of path for Concept_dimension is a sufficient answer to the protocol for data retrieval. LOINC semantics do not employ the hierarchical relationships in definition of the observable concept as does the SNOMED CT concept model and modifying the class hierarchy provided by Nathan for easier browsing of LOINC is not a matter of importance to the conceptual meaning of standard. Nonetheless, use of the LOINC standard for observables does require the leaf concept code 'LOINC: 21838-8’in the Concept_Dimension table for clinical observables. That is a required element for use of LOINC Jim ________________________________ From: Dan Connolly [[email protected]] Sent: Tuesday, May 27, 2014 10:21 AM To: [email protected]; Campbell, James R; [email protected] Cc: [email protected]; [email protected]; [email protected]; John Steinmetz Subject: RE: [gpc-informatics] #114: Milestone 2.7 GPC harmonizes with PCORI CDM V1.0 These documents still have SQL queries in them that directly constrain the observation_fact_table: Select Count(*) >From Observation_Fact Where Concept_CD = ‘LOINC: 21838-8’ (Ethnicity) My May 4 objection<http://listserv.kumc.edu/pipermail/gpc-dev/2014q2/000128.html> to this approach stands. i2b2 concept paths are necessary and sufficient; the generated sql from an i2b2 query using standardized paths may (a) indirect via the concept_dimension to map standard codes to local EMR codes; e.g. LOINC codes to local ethnicity codes and (b) may use other dimensions. The HERON ETL code currently results in (a) though not (b). -- Dan ________________________________________ From: GPC Informatics [[email protected]] Sent: Monday, May 26, 2014 9:52 AM To: [email protected]; Dan Connolly; [email protected] Cc: [email protected]; [email protected]; [email protected]; John Steinmetz Subject: 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, 67, 120 ----------------------------------------------+---------------------------- Comment (by campbell): During discussion two weeks ago, GPCDEV reached consensus on elements of the GPC standard model to align with PCORI CDM V1. I have revised the reference model presentation, added code sets where applicable to the data domains and updated the test SQL scripts for assessing CDM adherence. At the DSSNI meeting in Washington we were told that finalization of CDM would be issued shortly with response to the 210+ concerns that were submitted. The task force leader further stated that the Enrollment class in CDM was a placeholder for now and not to be concerned about details of implementing that feature of CDM for time being. Jim -- Ticket URL: <http://informatics.gpcnetwork.org/trac/Project/ticket/114#comment:14> gpc-informatics <http://informatics.gpcnetwork.org/> Greater Plains Network - Informatics 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.
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