Developer code to insert OMOP mappings.

dev/add_omop_codes.sql

@@ -1,6 +1,11 @@
 -- Working code to import OMOP codes into PCORnet ontology
 -- Only intended for developers
 -- Jeff Klann, PhD
+-- Presently only handles mappings of domainX to domainX. Some codes bifurcate and map a Condition to e.g., a Condition and an Observation
+-- Additionally only handles the codes of the expected type in the source tree. For example, codes that OMOP labels as Procedure in pcornet_diag have no mapping
+
+-- Do this at the start 
+update concept set invalid_reason=null where invalid_reason=''
 
 -- Add source code for condition (note: leaves out dxs that end up in measurement or observation
 update d set omop_sourcecode=concept_id
@@ -12,14 +17,27 @@ where
 c.domain_id='Condition'
 
 -- Fill in OMOP basecode for Condition
--- 9200 don't get converted that have a valid sourcecode...
-update d set omop_basecode=c1.concept_id
+-- 27,0000 don't get converted that have a valid sourcecode...
+update d set omop_basecode=c2.concept_id
+from pcornet_diag d inner join concept c1 on c1.concept_id=d.OMOP_SOURCECODE
+inner join   concept_relationship cr   ON  c1.concept_id = cr.concept_id_1 and cr.relationship_id = 'Maps to'
+inner join concept c2 ON c2.concept_id = cr.concept_id_2
+and c2.standard_concept = 'S'
+and c2.invalid_reason is null
+and c2.domain_id='Condition'
+
+-- Alternately, create new table for OMOP basecode for Condition
+-- Can handle multiple target SNOMED mappings this way
+
+select distinct omop_sourcecode,c2.concept_id,c2.domain_id into i2o_mapping
 from pcornet_diag d inner join concept c1 on c1.concept_id=d.OMOP_SOURCECODE
 inner join   concept_relationship cr   ON  c1.concept_id = cr.concept_id_1 and cr.relationship_id = 'Maps to'
 inner join concept c2 ON c2.concept_id = cr.concept_id_2
 and c2.standard_concept = 'S'
 and c2.invalid_reason is null
+--and c1.concept_id in (select omop_sourcecode from temp_mds)
 and c2.domain_id='Condition'
+--and c1.domain_id!=c2.domain_id
 
 -- Add source code for procedure (note: run with +1 and +0 in substring to catch basecode variations)
 update p set omop_sourcecode=concept_id
@@ -29,7 +47,6 @@ where
 c.domain_id='Procedure'
 
 -- Fill in OMOP basecode for Procedure
--- 9200 don't get converted that have a valid sourcecode...
 update d set omop_basecode=c1.concept_id
 from pcornet_proc d inner join concept c1 on c1.concept_id=d.OMOP_SOURCECODE
 inner join   concept_relationship cr   ON  c1.concept_id = cr.concept_id_1 and cr.relationship_id = 'Maps to'
@@ -38,6 +55,16 @@ and c2.standard_concept = 'S'
 and c2.invalid_reason is null
 and c2.domain_id='Procedure'
 
+-- Add to mapping table for Procedure
+insert into i2o_mapping(omop_sourcecode,concept_id,domain_id)
+select omop_sourcecode, c2.concept_id,c2.domain_id
+from pcornet_proc d inner join concept c1 on c1.concept_id=d.OMOP_SOURCECODE
+inner join   concept_relationship cr   ON  c1.concept_id = cr.concept_id_1 and cr.relationship_id = 'Maps to'
+inner join concept c2 ON c2.concept_id = cr.concept_id_2
+and c2.standard_concept = 'S'
+and c2.invalid_reason is null
+and c2.domain_id='Procedure'
+
 --- WORKSPACE ------
 
 select concept_id,concept_code,invalid_reason,domain_id,concept_name
@@ -50,4 +77,24 @@ omop_sourcecode is null and c.domain_id='Condition'
 select pcori_basecode,substring(pcori_basecode,charindex(':',pcori_basecode)+1,100) from pcornet_proc
 
 select * from concept_relationship cr inner join concept c on cr.concept_id_2=c.concept_id where c.standard_concept='S' and concept_id_1 in 
-(select omop_sourcecode from pcornet_diag where OMOP_BASECODE is  null and OMOP_SOURCECODE is not null)
+(select omop_sourcecode from pcornet_proc where OMOP_BASECODE is  null and OMOP_SOURCECODE is not null)
+
+select pcori_basecode from
+(select PCORI_BASECODE,count(*) c from
+(select distinct pcori_basecode,c2.concept_id from PCORNET_diag d inner join concept c1 on c1.concept_id=d.OMOP_SOURCECODE
+inner join   concept_relationship cr   ON  c1.concept_id = cr.concept_id_1 and cr.relationship_id = 'Maps to'
+inner join concept c2 ON c2.concept_id = cr.concept_id_2) x group by PCORI_BASECODE) x where c>1
+
+and c2.domain_id='Condition'
+where omop_basecode is null and omop_sourcecode is not null
+
+select distinct vocabulary_id,domain_id,invalid_reason from concept
+
+select * from PCORNET_DIAG where omop_basecode is null
+
+select * from pcornet_diag where m_applied_path!='@'
+
+select  condition_type_concept_id, count(*) from condition_occurrence group by condition_type_concept_id
+
+
+select * from pcornet_diag where omop_sourcecode=omop_basecode