From 2fad9ec50906e6e82de6f952cf73e685aa2743c4 Mon Sep 17 00:00:00 2001
From: schuemie <schuemie@ohdsi.org>
Date: Fri, 19 Aug 2016 12:09:08 +0200
Subject: [PATCH] Added specimen to stem table, with thanks to @ericaVoss

---
 .../dataModel/StemTableDefaultMappingV5.0.1.csv    | 14 ++++++++++++++
 .../rabbitInAHat/dataModel/StemTableV5.0.1.csv     |  5 +++++
 2 files changed, 19 insertions(+)

diff --git a/src/org/ohdsi/rabbitInAHat/dataModel/StemTableDefaultMappingV5.0.1.csv b/src/org/ohdsi/rabbitInAHat/dataModel/StemTableDefaultMappingV5.0.1.csv
index a6b7e10d..e1da56d5 100644
--- a/src/org/ohdsi/rabbitInAHat/dataModel/StemTableDefaultMappingV5.0.1.csv
+++ b/src/org/ohdsi/rabbitInAHat/dataModel/StemTableDefaultMappingV5.0.1.csv
@@ -91,3 +91,17 @@ STEM_TABLE,TYPE_CONCEPT_ID,DEATH,DEATH_TYPE_CONCEPT_ID
 STEM_TABLE,CONCEPT_ID,DEATH,CAUSE_CONCEPT_ID
 STEM_TABLE,SOURCE_VALUE,DEATH,CAUSE_SOURCE_VALUE
 STEM_TABLE,SOURCE_CONCEPT_ID,DEATH,CAUSE_SOURCE_CONCEPT_ID
+STEM_TABLE,PERSON_ID,SPECIMEN,PERSON_ID
+STEM_TABLE,CONCEPT_ID,SPECIMEN,SPECIMEN_CONCEPT_ID
+STEM_TABLE,TYPE_CONCEPT_ID,SPECIMEN,SPECIMEN_TYPE_CONCEPT_ID
+STEM_TABLE,START_DATE,SPECIMEN,SPECIMEN_DATE
+STEM_TABLE,START_TIME,SPECIMEN,SPECIMEN_TIME
+STEM_TABLE,QUANTITY,SPECIMEN,QUANTITY
+STEM_TABLE,UNIT_CONCEPT_ID,SPECIMEN,UNIT_CONCEPT_ID
+STEM_TABLE,ANATOMIC_SITE_CONCEPT_ID,SPECIMEN,ANATOMIC_SITE_CONCEPT_ID
+STEM_TABLE,DISEASE_STATUS_CONCEPT_ID,SPECIMEN,DISEASE_STATUS_CONCEPT_ID
+STEM_TABLE,SPECIMEN_SOURCE_ID,SPECIMEN,SPECIMEN_SOURCE_ID
+STEM_TABLE,SOURCE_VALUE,SPECIMEN,SPECIMEN_SOURCE_VALUE
+STEM_TABLE,UNIT_SOURCE_VALUE,SPECIMEN,UNIT_SOURCE_VALUE
+STEM_TABLE,ANATOMIC_SITE_SOURCE_VALUE,SPECIMEN,ANATOMIC_SITE_SOURCE_VALUE
+STEM_TABLE,DISEASE_STATUS_SOURCE_VALUE,SPECIMEN,DISEASE_STATUS_SOURCE_VALUE
diff --git a/src/org/ohdsi/rabbitInAHat/dataModel/StemTableV5.0.1.csv b/src/org/ohdsi/rabbitInAHat/dataModel/StemTableV5.0.1.csv
index c509e34f..a4fade39 100644
--- a/src/org/ohdsi/rabbitInAHat/dataModel/StemTableV5.0.1.csv
+++ b/src/org/ohdsi/rabbitInAHat/dataModel/StemTableV5.0.1.csv
@@ -35,3 +35,8 @@ STEM_TABLE,VALUE_AS_CONCEPT_ID,YES,INTEGER,"A foreign key to a result represente
 STEM_TABLE,VALUE_AS_NUMBER,YES,DECIMAL,A result where the result is expressed as a numeric value.
 STEM_TABLE,VALUE_AS_STRING,YES,CHARACTER VARYING,The result stored as a string. This is applicable where the result is expressed as verbatim text.
 STEM_TABLE,VALUE_SOURCE_VALUE,YES,CHARACTER VARYING,The source value associated with the content of the value_as_number or value_as_concept as stored in the source data.
+STEM_TABLE,ANATOMIC_SITE_CONCEPT_ID,YES,INTEGER,A foreign key to a Standard Concept identifier for the anatomic location of specimen collection.
+STEM_TABLE,DISEASE_STATUS_CONCEPT_ID,YES,INTEGER,A foreign key to a Standard Concept identifier for the Disease Status of specimen collection.
+STEM_TABLE,SPECIMEN_SOURCE_ID,YES,INTEGER,The Specimen identifier as it appears in the source data.
+STEM_TABLE,ANATOMIC_SITE_SOURCE_VALUE,YES,CHARACTER VARYING,The information about the anatomic site as detailed in the source.
+STEM_TABLE,DISEASE_STATUS_SOURCE_VALUE,YES,CHARACTER VARYING,The information about the disease status as detailed in the source.