Patch/followup 89 (#90)

* Allow multiple contraceptive use and not documented values * Add add'l reasons for surgery * Update regex * Build jsonld * Reorder columns * Build jsonld * Update regex * Build jsonld * Use marker status enum * Allow unknown * Workaround for age * Build jsonld * Allow HER2 to be more flexible for now * Build jsonld * Update contraceptive list * Fix and finalize * Build jsonld --------- Co-authored-by: gf-dcc-service <[email protected]>
gf-dcc · Feb 14, 2024 · de46d22 · de46d22
1 parent 49ec66c
commit de46d22
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Showing 8 changed files with 6,948 additions and 6,763 deletions.
diff --git a/GF.jsonld b/GF.jsonld
diff --git a/modules/classes/patient_and_specimen.yaml b/modules/classes/patient_and_specimen.yaml
@@ -27,8 +27,9 @@ classes:
     - Gravidity
     - Parity
     - AgeAtMenarche
-    - MenstrualCyclePhase
     - MenopauseStatus
+    - MenstrualCyclePhase
+    - ContraceptiveUseIndicator
     - TypeContraceptiveUse
     - DiagnosisStatusType
     - PreviousDiagnosis
@@ -59,6 +60,7 @@ classes:
     description: Group of individuals featured in the ovarian precancer atlas.
     slots:
     - MenstrualCyclePhase
+    - ContraceptiveUseIndicator
     - TypeContraceptiveUse
 
   PatientExtended:

diff --git a/modules/enums/Biospecimen.yaml b/modules/enums/Biospecimen.yaml
@@ -116,3 +116,4 @@ enums:
       Weakly Positive:
       Negative:
       Equivocal:
+      Unknown:
diff --git a/modules/enums/Demographics.yaml b/modules/enums/Demographics.yaml
@@ -300,13 +300,16 @@ enums:
       Tubal Sterilization:
       Ovarian Serous Cystadenoma:
       Endometriosis:
-      Uterine Fibroids: 
       'Uterine Fibroids + Endometriosis':
       'Uterine Fibroids + Adenomyosis':
+      Cervical Dysplasia:
       Cesarean Section:
       Menorrhagia:
       Adnexal Mass:
       Pelvic Mass:
+      Uterine Fibroids:
+      Uterine Lipoleiomyoma:
+      Uterine Prolapse:
       Unknown: 
 
   MenstrualCyclePhaseEnum:

diff --git a/modules/enums/Device.yaml b/modules/enums/Device.yaml
@@ -40,16 +40,20 @@ enums:
       Oral:
       Oral (estrogen):
       Oral (progesterone):
+      Oral (estrogen/progesterone):
       Male sterilization:
       Condoms:
+      Diaphragm:
       Patch:
+      Patch (progesterone):
       Vaginal ring:
+      Vaginal ring (estrogen/progesterone):
       IUD:
       IUD (progesterone):
       Implant:
       Implant (progesterone):
       Injection (progesterone):
       Bilateral tubal ligation:
       Natural family planning:
-      Unknown:
-
+      Rhythm:
+      Not Documented: