Merge pull request #182 from OHDSI/conceptFileFix

Update to concept check file to remove a duplicate that was causing a…

inst/csv/OMOP_CDMv5.3.1_Concept_Level.csv

@@ -113,8 +113,7 @@ CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,200675,Neoplasm of uncertain behavior
 CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,200775,Endometrial hyperplasia,,,,,,,,,Female,5,,,,,,,,,,
 CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,200779,Polyp of corpus uteri,,,,,,,,,Female,5,,,,,,,,,,
 CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,200780,Disorder of uterus,,,,,,,,,Female,5,,,,,,,,,,
-CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,200962,Primary malignant neoplasm of prostate,,,,,,,,,Male,5,,,,,,,,,,
-CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,200962,Primary malignant neoplasm of prostate,,,,,,,,,,,,Yes,,,0.0052,,,0.0471,,
+CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,200962,Primary malignant neoplasm of prostate,,,,,,,,,Male,5,,Yes,,,0.0052,,,0.0471,,
 CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,200970,Carcinoma in situ of prostate,,,,,,,,,Male,5,,,,,,,,,,
 CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,201072,Benign prostatic hypertrophy without outflow obstruction,,,,,,,,,Male,5,,,,,,,,,,
 CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,201078,Atrophic vaginitis,,,,,,,,,Female,5,,,,,,,,,,
@@ -198,7 +197,7 @@ PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2109833,"Laser vaporization of prostat
 PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2109900,"Destruction of lesion(s), penis (eg, condyloma, papilloma, molluscum contagiosum, herpetic vesicle), simple; chemical",,,,,,,,,Male,5,,,,,,,,,,
 PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2109902,"Destruction of lesion(s), penis (eg, condyloma, papilloma, molluscum contagiosum, herpetic vesicle), simple; cryosurgery",,,,,,,,,Male,5,,,,,,,,,,
 PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2109905,"Destruction of lesion(s), penis (eg, condyloma, papilloma, molluscum contagiosum, herpetic vesicle), extensive (eg, laser surgery, electrosurgery, cryosurgery, chemosurgery)",,,,,,,,,Male,5,,,,,,,,,,
-PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2109906,Biopsy of penis, (separate procedure),,,,,,,,Male,5,,,,,,,,,,
+PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2109906,"Biopsy of penis, (separate procedure)",,,,,,,,,Male,5,,,,,,,,,,
 PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2109916,"Circumcision, using clamp or other device with regional dorsal penile or ring block",,,,,,,,,Male,5,,,,,,,,,,
 PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2109968,Foreskin manipulation including lysis of preputial adhesions and stretching,,,,,,,,,Male,5,,,,,,,,,,
 PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2109973,"Orchiectomy, simple (including subcapsular), with or without testicular prosthesis, scrotal or inguinal approach",,,,,,,,,Male,5,,,,,,,,,,
@@ -211,7 +210,7 @@ PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2110044,"Laparoscopy, surgical prostat
 PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2110078,Colposcopy of the vulva,,,,,,,,,Female,5,,,,,,,,,,
 PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2110116,"Colpopexy, vaginal; extra-peritoneal approach (sacrospinous, iliococcygeus)",,,,,,,,,Female,5,,,,,,,,,,
 PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2110142,"Laparoscopy, surgical, colpopexy (suspension of vaginal apex)",,,,,,,,,Female,5,,,,,,,,,,
-PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2110144,Colposcopy of the cervix including upper/adjacent vagina, with biopsy(s) of the cervix and endocervical curettage,,,,,,,,Female,5,,,,,,,,,,
+PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2110144,"Colposcopy of the cervix including upper/adjacent vagina, with biopsy(s) of the cervix and endocervical curettage",,,,,,,,,Female,5,,,,,,,,,,
 PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2110169,"Endometrial sampling (biopsy) with or without endocervical sampling (biopsy), without cervical dilation, any method (separate procedure)",,,,,,,,,Female,5,,,,,,,,,,
 PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2110175,"Total abdominal hysterectomy (corpus and cervix), with or without removal of tube(s), with or without removal of ovary(s)",,,,,,,,,Female,5,,,,,,,,,,
 PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2110194,Insertion of intrauterine device (IUD),,,,,,,,,Female,5,,,,,,,,,,
@@ -223,7 +222,7 @@ PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2110230,"Laparoscopy, surgical, with t
 PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2110307,"Routine obstetric care including antepartum care, vaginal delivery (with or without episiotomy, and/or forceps) and postpartum care",,,,,,,,,Female,5,,,,,,,,,,
 PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2110315,"Routine obstetric care including antepartum care, cesarean delivery, and postpartum care",,,,,,,,,Female,5,,,,,,,,,,
 PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2110316,Cesarean delivery only,,,,,,,,,Female,5,,,,,,,,,,
-PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2110317,Cesarean delivery only, including postpartum care,,,,,,,,Female,5,,,,,,,,,,
+PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2110317,"Cesarean delivery only, including postpartum care",,,,,,,,,Female,5,,,,,,,,,,
 PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2110326,"Treatment of missed abortion, completed surgically; first trimester",,,,,,,,,Female,5,,,,,,,,,,
 PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2211747,"Ultrasound, pregnant uterus, real time with image documentation, fetal and maternal evaluation, first trimester (< 14 weeks 0 days), transabdominal approach; single or first gestation",,,,,,,,,Female,5,,,,,,,,,,
 PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2211749,"Ultrasound, pregnant uterus, real time with image documentation, fetal and maternal evaluation, after first trimester (> or = 14 weeks 0 days), transabdominal approach; single or first gestation",,,,,,,,,Female,5,,,,,,,,,,
@@ -306,7 +305,7 @@ MEASUREMENT,MEASUREMENT_CONCEPT_ID,2212643,Blood count; hemoglobin (Hgb),8713,gr
 MEASUREMENT,MEASUREMENT_CONCEPT_ID,2212643,Blood count; hemoglobin (Hgb),8837,microgram per deciliter,2,5,,319,5,,,,,,,,,,,,,
 MEASUREMENT,MEASUREMENT_CONCEPT_ID,2212643,Blood count; hemoglobin (Hgb),8840,milligram per deciliter,3,5,,36,5,,,,,,,,,,,,,
 MEASUREMENT,MEASUREMENT_CONCEPT_ID,2212742,"Thromboplastin time, partial (PTT); plasma or whole blood",8554,percent,0,5,,100,5,,,,,,,,,,,,,
-PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2617204,Cervical or vaginal cancer screening, pelvic and clinical breast examination,,,,,,,,Female,5,,,,,,,,,,
+PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2617204,"Cervical or vaginal cancer screening, pelvic and clinical breast examination",,,,,,,,Female,5,,,,,,,,,,,
 PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2721063,"Annual gynecological examination, new patient",,,,,,,,,Female,5,,,,,,,,,,
 PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2721064,"Annual gynecological examination, established patient",,,,,,,,,Female,5,,,,,,,,,,
 PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,2780478,"Resection of Prostate, Percutaneous Endoscopic Approach",,,,,,,,,Male,5,,,,,,,,,,
@@ -602,7 +601,7 @@ MEASUREMENT,MEASUREMENT_CONCEPT_ID,3013429,Basophils [#/volume] in Blood by Auto
 MEASUREMENT,MEASUREMENT_CONCEPT_ID,3013429,Basophils [#/volume] in Blood by Automated count,8816,million per milliliter,0,5,,1,5,,,,,,,,,,,,,
 MEASUREMENT,MEASUREMENT_CONCEPT_ID,3013429,Basophils [#/volume] in Blood by Automated count,8848,thousand per microliter,0,5,,400,5,,,,,,,,,,,,,
 MEASUREMENT,MEASUREMENT_CONCEPT_ID,3013429,Basophils [#/volume] in Blood by Automated count,8961,thousand per cubic millimeter,0,5,,400,5,,,,,,,,,,,,,
-MEASUREMENT,MEASUREMENT_CONCEPT_ID,3013429,Basophils [#/volume] in Blood by Automated count,9254,per liter,0,5,,4E+11,5,,,,,,,,,,,,,
+MEASUREMENT,MEASUREMENT_CONCEPT_ID,3013429,Basophils [#/volume] in Blood by Automated count,9254,per liter,0,5,,4.00E+11,5,,,,,,,,,,,,,
 MEASUREMENT,MEASUREMENT_CONCEPT_ID,3013429,Basophils [#/volume] in Blood by Automated count,9435,thousand per liter,0,5,,400000000,5,,,,,,,,,,,,,
 MEASUREMENT,MEASUREMENT_CONCEPT_ID,3013429,Basophils [#/volume] in Blood by Automated count,9436,thousand per milliliter,0,5,,400000,5,,,,,,,,,,,,,
 MEASUREMENT,MEASUREMENT_CONCEPT_ID,3013429,Basophils [#/volume] in Blood by Automated count,9444,billion per liter,0,5,,400,5,,,,,,,,,,,,,

inst/csv/OMOP_CDMv5.3.1_Field_Level.csv

@@ -64,7 +64,7 @@ CONDITION_OCCURRENCE,visit_detail_id,No,,,integer,0,,,,No,,,Yes,0,,VISIT_DETAIL,
 CONDITION_OCCURRENCE,condition_source_value,No,,,varchar(50),0,,"This field is discouraged from use in analysis because it is not required to contain Standard Concepts that are used across the OHDSI community, and should only be used when Standard Concepts do not adequately represent the source detail for the Condition necessary for a given analytic use case.  Consider using CONDITION_CONCEPT_ID instead to enable standardized analytics that can be consistent across the network.  ",This code is mapped to a Standard Condition Concept in the Standardized Vocabularies and the original code is stored here for reference.,No,,,No,,,,,,,,,,,No,,,Yes,100,,No,,,No,,,Yes,10,,CONDITION_CONCEPT_ID,,,,,,,,,,,,No,,,Yes
 CONDITION_OCCURRENCE,condition_source_concept_id,No,,,integer,0,,,,No,,,Yes,0,,CONCEPT,CONCEPT_ID,,,,,,,No,,,Yes,100,,No,,,Yes,10,,No,,,,,,,,,,,,,,,No,,,Yes
 CONDITION_OCCURRENCE,condition_status_source_value,No,,,varchar(50),0,,,This code is mapped to a Standard Concept in the Standardized Vocabularies and the original code is stored here for reference.,No,,,No,,,,,,,,,,,No,,,Yes,100,,No,,,No,,,Yes,100,,CONDITION_STATUS_CONCEPT_ID,,,,,,,,,,,,No,,,Yes
-DRUG_EXPOSURE,drug_exposure_id,Yes,0,,bigint,0,,,,Yes,,,No,,,,,,,,,,,No,,,Yes,0,,No,,,No,,,No,,,,,,,,,,,,,,,No,,,Yes
+DRUG_EXPOSURE,drug_exposure_id,Yes,0,,bigint,0,,,,Yes,0,,No,,,,,,,,,,,No,,,Yes,0,,No,,,No,,,No,,,,,,,,,,,,,,,No,,,Yes
 DRUG_EXPOSURE,person_id,Yes,0,,bigint,0,,,,No,,,Yes,0,,PERSON,PERSON_ID,,,,,,,No,,,Yes,0,,No,,,No,,,No,,,,,,,,,,,,,,,No,,,Yes
 DRUG_EXPOSURE,drug_concept_id,Yes,0,,integer,0,,,,No,,,Yes,0,,CONCEPT,CONCEPT_ID,Drug,0,,,,,Yes,0,,Yes,0,,Yes,5,,No,,,No,,,,,,,,,,,,,,,No,,,Yes
 DRUG_EXPOSURE,drug_exposure_start_date,Yes,0,,date,0,,,"Valid entries include a start date of a prescription, the date a prescription was filled, or the date on which a Drug administration procedure was recorded.",No,,,No,,,,,,,,,,,No,,,Yes,0,,No,,,No,,,No,,,,'1950-01-01',1,,"DATEADD(dd,1,GETDATE())",1,,Yes,PERSON,BIRTH_DATETIME,1,,Yes,1,,Yes