Add logic to support SDoH concept's categorical answer code map.

stephanieshong commented 2 years ago

The column where the answer code is submitted will be different for each CDM.

OBS_GEN with LOINC codes in obsgen_result_text
LC obsgen_type mean LOINC codes. These entries should be added to the p2o xw tables to have the matching entries for code translations
so far all categorical result text has been plain English text that we need to match on to translate to value_as_concept_ids. With the SDoH data, the categorical answer texts are coming in as the LOINC answer codes in the obsgen_result_text. Generate a table to translate all possible answer codes and join this xw table to retrieve the valid value_as_concept_ids. answer_code_xw dataset is generated before the domain mapping step.
in the final observation table union data from the obs_gen
p2o_valueset_mapping table with obsgen_source valuesets
SDoH data in OBS_GEN added to the Observation domain

LAB_RESULT with SDoH LOINC codes and the LOINC coded answer code in the text_result_val

ACT CDM will submit SDoH question's answers in the LOINC coded format in the valueflag_cd column of the observation_fact table. Generate the answer code mapping table prior to the mapping step.

stephanieshong commented 2 years ago

PCORnet CDM code change merged to template source. Waiting on deployment

stephanieshong commented 2 years ago

PCORnet CDM pull request with SDoH changes are merged.

stephanieshong commented 2 years ago

ACT CDM - Use generated SDoH answer concepts codes xwalk table if site is sending the LOINC coded answer codes in the valueflag_cd column in the observation_fact table. PR is here: https://unite.nih.gov/workspace/data-integration/code/repos/ri.stemma.main.repository.9c930d2f-ad52-41c2-bbf6-b4fd137c56d4/pulls Done.

stephanieshong commented 2 years ago

[x] PCORNet obsgen/obgen_result_text
[x] ACT - observation_fact/valueflag_cd - use the valueset mapping table first and then the answer_code_xwalk mapping file
[x] TriNetX - text_result_val will have the LOINC coded answer text - try to use the valueset_mapping_xwalk first, if not then try to use the sdoh_answer_code_xwalk to map the concept_ids

stephanieshong commented 2 years ago

all PRs merged.

National-COVID-Cohort-Collaborative / Data-Ingestion-and-Harmonization