Merge pull request #33 from mcwdsi/fix-dose-forms

Fix dose forms for clinical drug forms
mcwdsi · Jul 27, 2024 · a1274b1 · a1274b1
2 parents 1cb7ad6 + a10d7e5
commit a1274b1
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Showing 6 changed files with 185 additions and 98 deletions.
diff --git a/src/ontology/dron.Makefile b/src/ontology/dron.Makefile
@@ -24,7 +24,7 @@ $(IMPORTDIR)/uo_import.owl: $(MIRRORDIR)/uo.owl $(IMPORTDIR)/uo_terms_combined.t
 # (no NDC) and the run a regular full release.
 
 LITE_ARTEFACTS=$(COMPONENTSDIR)/dron-rxnorm.owl $(COMPONENTSDIR)/dron-ingredient.owl $(COMPONENTSDIR)/dron-obsolete.owl $(IMPORT_OWL_FILES)
-$(TMPDIR)/dron-edit_lite.owl: $(SRC) $(LITE_ARTEFACTS)
+$(TMPDIR)/dron-edit_lite.owl: $(SRC) $(LITE_ARTEFACTS) | $(TMPDIR)/
 	$(ROBOT) remove --input $(SRC) --select imports \
 	merge $(patsubst %, -i %, $(LITE_ARTEFACTS)) --output $@.tmp.owl && mv $@.tmp.owl $@
 
@@ -45,7 +45,7 @@ $(TMPDIR)/ldtab.jar: | $(TMPDIR)
 LDTAB := java -jar $(TMPDIR)/ldtab.jar
 
 # Load DrOn templates into SQLite.
-$(TMPDIR)/dron.db: $(SCRIPTSDIR)/create-dron-tables.sql $(SCRIPTSDIR)/load-dron-tables.sql $(SCRIPTSDIR)/index-dron-tables.sql $(TEMPLATEDIR)/*.tsv
+$(TMPDIR)/dron.db: $(SCRIPTSDIR)/create-dron-tables.sql $(SCRIPTSDIR)/load-dron-tables.sql $(SCRIPTSDIR)/index-dron-tables.sql $(TEMPLATEDIR)/*.tsv | $(TMPDIR)/
 	rm -f $@
 	sqlite3 $@ < $<
 	sqlite3 $@ < $(word 2,$^)

diff --git a/src/scripts/create-dron-tables.sql b/src/scripts/create-dron-tables.sql
@@ -113,6 +113,12 @@ CREATE TABLE unit (
     ontology_label TEXT UNIQUE NOT NULL
 );
 
+CREATE TABLE dose_form (
+    rxcui INTEGER PRIMARY KEY NOT NULL,
+    label TEXT UNIQUE NOT NULL,
+    curie TEXT NOT NULL
+);
+
 -- Create triggers for automatically assigning DRON IDs.
 -- First create a table with one row to track the current ID.
 CREATE TABLE current_dron_id ( id INTEGER );

diff --git a/src/scripts/load-dron-tables.sql b/src/scripts/load-dron-tables.sql
@@ -20,6 +20,7 @@ PRAGMA foreign_keys = ON;
 .import --skip 1 ../templates/ndc_clinical_drug.tsv ndc_clinical_drug
 .import --skip 1 ../templates/obsolete.tsv obsolete
 .import --skip 1 ../templates/unit.tsv unit
+.import --skip 1 ../templates/dose_form.tsv dose_form
 
 -- Set current_dron_id.
 DELETE FROM current_dron_id;

diff --git a/src/scripts/update-dron-from-rxnorm.sql b/src/scripts/update-dron-from-rxnorm.sql
@@ -11,11 +11,15 @@ DROP TABLE IF EXISTS new_clinical_drug_form;
 CREATE TABLE new_clinical_drug_form AS
 SELECT
   RXCUI AS rxcui,
-  STR AS label
-FROM rxnorm.RXNCONSO
-WHERE SAB = 'RXNORM'
-  AND TTY = 'SCDF'
-  AND RXCUI NOT IN (SELECT rxcui FROM dron.clinical_drug_form);
+  STR AS label,
+  COALESCE(df.curie, 'DRON:00000005') AS parent -- default 'drug product'
+FROM rxnorm.RXNCONSO AS c
+LEFT JOIN rxnorm.RXNREL AS r ON r.RXCUI2 = c.RXCUI
+LEFT JOIN dron.dose_form AS df ON r.RXCUI1 = df.rxcui
+WHERE c.SAB = 'RXNORM'
+  AND c.TTY = 'SCDF'
+  AND c.RXCUI NOT IN (SELECT rxcui FROM dron.clinical_drug_form)
+  AND r.RELA = 'has_dose_form';
 
 -- Find new clinical drugs.
 DROP TABLE IF EXISTS new_clinical_drug;
@@ -120,7 +124,7 @@ INSERT INTO dron.clinical_drug_form
 SELECT
   NULL AS curie,
   label AS label,
-  NULL AS parent,
+  parent AS parent,
   rxcui AS rxcui
 FROM new_clinical_drug_form;