diff --git a/src/ontology/catalog-v001.xml b/src/ontology/catalog-v001.xml
index 9bdfdfa..4cf5084 100644
--- a/src/ontology/catalog-v001.xml
+++ b/src/ontology/catalog-v001.xml
@@ -29,6 +29,7 @@
-
+
+
-
\ No newline at end of file
+
diff --git a/src/ontology/dron-edit.owl b/src/ontology/dron-edit.owl
index 618ccc0..a531983 100644
--- a/src/ontology/dron-edit.owl
+++ b/src/ontology/dron-edit.owl
@@ -12,6 +12,7 @@ Ontology(
Import()
Import()
Import()
+Import()
Import()
Import()
Import()
@@ -2160,4 +2161,4 @@ AnnotationAssertion( "ciara lusnia")
-)
\ No newline at end of file
+)
diff --git a/src/ontology/dron.Makefile b/src/ontology/dron.Makefile
index 89d9c5a..f0642f2 100644
--- a/src/ontology/dron.Makefile
+++ b/src/ontology/dron.Makefile
@@ -11,7 +11,7 @@
# In essence we merge rxnorm, dron-ingredient, all imports and the edit file
# (no NDC) and the run a regular full release.
-LITE_ARTEFACTS=$(COMPONENTSDIR)/dron-rxnorm.owl $(COMPONENTSDIR)/dron-ingredient.owl $(IMPORT_OWL_FILES)
+LITE_ARTEFACTS=$(COMPONENTSDIR)/dron-rxnorm.owl $(COMPONENTSDIR)/dron-ingredient.owl $(COMPONENTSDIR)/dron-obsolete.owl $(IMPORT_OWL_FILES)
$(TMPDIR)/dron-edit_lite.owl: $(SRC) $(LITE_ARTEFACTS)
$(ROBOT) remove --input $(SRC) --select imports \
merge $(patsubst %, -i %, $(LITE_ARTEFACTS)) --output $@.tmp.owl && mv $@.tmp.owl $@
@@ -33,13 +33,14 @@ $(TMPDIR)/ldtab.jar: | $(TMPDIR)
LDTAB := java -jar $(TMPDIR)/ldtab.jar
# Load DrOn templates into SQLite.
-$(TMPDIR)/dron.db: $(SCRIPTSDIR)/create-dron-tables.sql $(SCRIPTSDIR)/load-dron-tables.sql
+$(TMPDIR)/dron.db: $(SCRIPTSDIR)/create-dron-tables.sql $(SCRIPTSDIR)/load-dron-tables.sql $(SCRIPTSDIR)/index-dron-tables.sql
rm -f $@
sqlite3 $@ < $<
sqlite3 $@ < $(word 2,$^)
+ sqlite3 $@ < $(word 3,$^)
# Load ChEBI into SQLite using LDTab.
-$(TMPDIR)/chebi.db: $(SCRIPTSDIR)/prefix.tsv $(TMPDIR)/mirror-chebi.owl | $(TMPDIR)/ldtab.jar
+$(TMPDIR)/chebi.db: $(SCRIPTSDIR)/prefix.tsv $(TMPDIR)/mirror-chebi.owl $(SCRIPTSDIR)/collect-chebi-labels.sql | $(TMPDIR)/ldtab.jar
$(eval DB=$@)
rm -f $@
$(LDTAB) init $(DB) --table chebi
@@ -48,6 +49,8 @@ $(TMPDIR)/chebi.db: $(SCRIPTSDIR)/prefix.tsv $(TMPDIR)/mirror-chebi.owl | $(TMPD
sqlite3 $(DB) "CREATE INDEX idx_chebi_subject ON chebi(subject)"
sqlite3 $(DB) "CREATE INDEX idx_chebi_predicate ON chebi(predicate)"
sqlite3 $(DB) "CREATE INDEX idx_chebi_object ON chebi(object)"
+ sqlite3 $(DB) "ANALYZE"
+ sqlite3 $(DB) < $(word 3,$^)
# Create a SQLite database for RxNorm and load data from tmp/rxnorm/*.RRF.
$(TMPDIR)/rxnorm.db: $(SCRIPTSDIR)/create-rxnorm-tables.sql $(SCRIPTSDIR)/load-rxnorm-tables.sql $(SCRIPTSDIR)/index-rxnorm-tables.sql | $(TMPDIR)/
@@ -61,6 +64,15 @@ update-labels: $(TMPDIR)/dron.db $(TMPDIR)/chebi.db $(TMPDIR)/rxnorm.db $(SCRIPT
sqlite3 < $(word 4,$^)
cd $(TEMPLATEDIR) && sqlite3 ../ontology/$< < ../ontology/$(word 5,$^)
+.PHONY: update-rxnorm
+update-rxnorm: $(TMPDIR)/dron.db $(TMPDIR)/chebi.db $(TMPDIR)/rxnorm.db $(SCRIPTSDIR)/update-dron-from-rxnorm.sql $(SCRIPTSDIR)/save-dron-tables.sql
+ sqlite3 < $(word 4,$^)
+ cd $(TEMPLATEDIR) && sqlite3 ../ontology/$< < ../ontology/$(word 5,$^)
+
+# Report common problems.
+$(TMPDIR)/problems.db: $(TMPDIR)/dron.db $(TMPDIR)/chebi.db $(TMPDIR)/rxnorm.db $(SCRIPTSDIR)/report-problems.sql
+ sqlite3 $@ < $(word 4,$^)
+
# Convert DrOn template tables to LDTab format tables.
$(TMPDIR)/ldtab.db: $(TMPDIR)/dron.db $(SCRIPTSDIR)/prefix.tsv $(SCRIPTSDIR)/convert-dron-ldtab.sql | $(TMPDIR)/ldtab.jar
$(eval DB=$@)
@@ -68,6 +80,7 @@ $(TMPDIR)/ldtab.db: $(TMPDIR)/dron.db $(SCRIPTSDIR)/prefix.tsv $(SCRIPTSDIR)/con
$(LDTAB) init $(DB) --table dron_ingredient
$(LDTAB) init $(DB) --table dron_rxnorm
$(LDTAB) init $(DB) --table dron_ndc
+ $(LDTAB) init $(DB) --table dron_obsolete
$(LDTAB) prefix $@ $(word 2,$^)
sqlite3 $@ < $(word 3,$^)
@@ -81,7 +94,7 @@ $(COMPONENTSDIR)/%.owl: $(COMPONENTSDIR)/%.ttl
$(ROBOT) convert -i $< -o $@
# Override the all_components task.
-all_components: $(COMPONENTSDIR)/dron-ingredient.ttl $(COMPONENTSDIR)/dron-rxnorm.ttl $(COMPONENTSDIR)/dron-ndc.ttl $(COMPONENTSDIR)/dron-ingredient.owl $(COMPONENTSDIR)/dron-rxnorm.owl $(COMPONENTSDIR)/dron-ndc.owl
+all_components: $(COMPONENTSDIR)/dron-ingredient.ttl $(COMPONENTSDIR)/dron-rxnorm.ttl $(COMPONENTSDIR)/dron-ndc.ttl $(COMPONENTSDIR)/dron-obsolete.ttl $(COMPONENTSDIR)/dron-ingredient.owl $(COMPONENTSDIR)/dron-rxnorm.owl $(COMPONENTSDIR)/dron-ndc.owl $(COMPONENTSDIR)/dron-obsolete.owl
###################################
#### Create templates from OWL ####
@@ -99,17 +112,19 @@ $(TMPDIR)/reverse/:
$(TMPDIR)/reverse/dron-%.owl: components.bk/dron-%.owl | $(TMPDIR)/reverse/
$(ROBOT) convert -i $< -o $@
-$(TMPDIR)/reverse.db: $(SCRIPTSDIR)/prefix.tsv $(SCRIPTSDIR)/create-dron-tables.sql $(SCRIPTSDIR)/convert-ldtab-dron.sql $(TMPDIR)/reverse/dron-ingredient.owl $(TMPDIR)/reverse/dron-rxnorm.owl $(TMPDIR)/reverse/dron-ndc.owl | $(TMPDIR)/ldtab.jar
+$(TMPDIR)/reverse.db: $(SCRIPTSDIR)/prefix.tsv $(SCRIPTSDIR)/create-dron-tables.sql $(SCRIPTSDIR)/convert-ldtab-dron.sql $(TMPDIR)/reverse/dron-ingredient.owl $(TMPDIR)/reverse/dron-rxnorm.owl $(TMPDIR)/reverse/dron-ndc.owl $(TMPDIR)/reverse/dron-obsolete.owl | $(TMPDIR)/ldtab.jar
$(eval DB=$@)
rm -f $(DB)
$(LDTAB) init $(DB) --table dron_ingredient
$(LDTAB) init $(DB) --table dron_rxnorm
$(LDTAB) init $(DB) --table dron_ndc
+ $(LDTAB) init $(DB) --table dron_obsolete
$(LDTAB) prefix $(DB) $<
sqlite3 $(DB) < $(word 2,$^)
$(LDTAB) import $(DB) --table dron_ingredient $(TMPDIR)/reverse/dron-ingredient.owl
$(LDTAB) import $(DB) --table dron_rxnorm $(TMPDIR)/reverse/dron-rxnorm.owl
$(LDTAB) import $(DB) --table dron_ndc $(TMPDIR)/reverse/dron-ndc.owl
+ $(LDTAB) import $(DB) --table dron_obsolete $(TMPDIR)/reverse/dron-obsolete.owl
.PHONY: reverse
reverse: $(TMPDIR)/reverse.db $(SCRIPTSDIR)/save-dron-tables.sql
@@ -143,4 +158,4 @@ $(TMPDIR)/%.owl.diff: $(TMPDIR)/reverse/%.owl $(COMPONENTSDIR)/%.owl
-diff -u $^ > $@
.PHONY: roundtrip
-roundtrip: $(COMPONENTSDIR)/dron-ingredient.ttl $(COMPONENTSDIR)/dron-rxnorm.ttl $(COMPONENTSDIR)/dron-ndc.ttl $(TMPDIR)/dron-ingredient.owl.diff $(TMPDIR)/dron-ingredient.tsv.diff $(TMPDIR)/dron-rxnorm.owl.diff $(TMPDIR)/dron-rxnorm.tsv.diff $(TMPDIR)/dron-ndc.owl.diff $(TMPDIR)/dron-ndc.tsv.diff
+roundtrip: $(COMPONENTSDIR)/dron-ingredient.ttl $(COMPONENTSDIR)/dron-rxnorm.ttl $(COMPONENTSDIR)/dron-ndc.ttl $(COMPONENTSDIR)/dron-obsolete.ttl $(TMPDIR)/dron-ingredient.owl.diff $(TMPDIR)/dron-ingredient.tsv.diff $(TMPDIR)/dron-rxnorm.owl.diff $(TMPDIR)/dron-rxnorm.tsv.diff $(TMPDIR)/dron-ndc.owl.diff $(TMPDIR)/dron-ndc.tsv.diff $(TMPDIR)/dron-obsolete.owl.diff $(TMPDIR)/dron-obsolete.tsv.diff
diff --git a/src/scripts/collect-chebi-labels.sql b/src/scripts/collect-chebi-labels.sql
new file mode 100644
index 0000000..6480a43
--- /dev/null
+++ b/src/scripts/collect-chebi-labels.sql
@@ -0,0 +1,20 @@
+-- Collect labels from ChEBI terms that are not deprecated.
+DROP TABLE IF EXISTS label;
+CREATE TABLE label (
+ curie TEXT PRIMARY KEY,
+ label TEXT UNIQUE
+);
+
+INSERT OR IGNORE INTO label
+SELECT
+ subject AS curie,
+ object AS label
+FROM chebi
+WHERE predicate = 'rdfs:label'
+ AND subject NOT IN (
+ SELECT subject
+ FROM chebi
+ WHERE predicate = 'owl:deprecated'
+ );
+CREATE INDEX idx_label_label ON label(label);
+ANALYZE label;
diff --git a/src/scripts/convert-dron-ldtab.sql b/src/scripts/convert-dron-ldtab.sql
index 23c4951..9674326 100644
--- a/src/scripts/convert-dron-ldtab.sql
+++ b/src/scripts/convert-dron-ldtab.sql
@@ -474,3 +474,38 @@ FROM (
UNION
SELECT curie, clinical_drug AS drug FROM dron.ndc_clinical_drug
);
+
+
+-- ## Obsolete Terms
+
+INSERT OR IGNORE INTO dron_obsolete(subject, predicate, object)
+SELECT
+ curie AS subject,
+ 'rdf:type' AS predicate,
+ type AS object
+FROM obsolete;
+
+INSERT OR IGNORE INTO dron_obsolete(subject, predicate, object, datatype)
+SELECT
+ curie AS subject,
+ 'rdfs:label' AS predicate,
+ label AS object,
+ 'xsd:string' AS datatype
+FROM obsolete;
+
+INSERT OR IGNORE INTO dron_obsolete(subject, predicate, object, datatype)
+SELECT
+ curie AS subject,
+ 'owl:deprecated' AS predicate,
+ 'true' AS object,
+ 'xsd:boolean' AS datatype
+FROM obsolete;
+
+INSERT OR IGNORE INTO dron_obsolete(subject, predicate, object)
+SELECT
+ curie AS subject,
+ 'IAO:0100001' AS predicate,
+ replaced_by AS object
+FROM obsolete
+WHERE replaced_by IS NOT NULL
+ AND replaced_by != '';
diff --git a/src/scripts/convert-ldtab-dron.sql b/src/scripts/convert-ldtab-dron.sql
index 836edc3..bc478a9 100644
--- a/src/scripts/convert-ldtab-dron.sql
+++ b/src/scripts/convert-ldtab-dron.sql
@@ -174,3 +174,22 @@ UNION
SELECT rxcui FROM clinical_drug
UNION
SELECT rxcui FROM branded_drug;
+
+
+-- ## dron-obsolete
+
+INSERT OR IGNORE INTO obsolete(curie, label, type)
+SELECT
+ a.subject AS curie,
+ b.object AS label,
+ a.object AS type
+FROM dron_obsolete AS a
+LEFT JOIN dron_obsolete AS b ON a.subject = b.subject
+WHERE a.predicate = 'rdf:type'
+ AND b.predicate = 'rdfs:label';
+
+UPDATE obsolete
+SET replaced_by = object
+FROM dron_obsolete
+WHERE obsolete.curie = dron_obsolete.subject
+ AND dron_obsolete.predicate = 'IAO:0100001';
diff --git a/src/scripts/create-dron-tables.sql b/src/scripts/create-dron-tables.sql
index ca4cff9..52896d5 100644
--- a/src/scripts/create-dron-tables.sql
+++ b/src/scripts/create-dron-tables.sql
@@ -1,104 +1,116 @@
-- Create the DrOn tables.
CREATE TABLE rxcui (
- rxcui INT PRIMARY KEY,
+ rxcui INTEGER PRIMARY KEY NOT NULL,
replaced_by INTEGER
);
CREATE TABLE disposition (
curie TEXT PRIMARY KEY,
- label TEXT UNIQUE
+ label TEXT UNIQUE NOT NULL
);
CREATE TABLE ingredient (
curie TEXT PRIMARY KEY,
- label TEXT, -- UNIQUE,
- rxcui INTEGER,
+ label TEXT NOT NULL,
+ rxcui INTEGER NOT NULL,
FOREIGN KEY (rxcui) REFERENCES rxcui(rxcui)
);
CREATE TABLE ingredient_disposition (
- ingredient TEXT,
- disposition TEXT,
+ ingredient TEXT NOT NULL,
+ disposition TEXT NOT NULL,
FOREIGN KEY (ingredient) REFERENCES ingredient(curie),
FOREIGN KEY (disposition) REFERENCES disposition(curie)
);
CREATE TABLE clinical_drug_form (
curie TEXT PRIMARY KEY,
- label TEXT, -- UNIQUE,
+ label TEXT NOT NULL, -- UNIQUE,
parent TEXT,
- rxcui INTEGER,
+ rxcui INTEGER NOT NULL,
FOREIGN KEY (rxcui) REFERENCES rxcui(rxcui)
);
CREATE TABLE clinical_drug_form_ingredient (
- clinical_drug_form TEXT,
- ingredient TEXT,
+ clinical_drug_form TEXT NOT NULL,
+ ingredient TEXT NOT NULL,
+ PRIMARY KEY (clinical_drug_form, ingredient),
FOREIGN KEY (clinical_drug_form) REFERENCES clinical_drug_form(curie),
FOREIGN KEY (ingredient) REFERENCES ingredient(curie)
);
CREATE TABLE clinical_drug_form_disposition (
- clinical_drug_form TEXT,
- disposition TEXT,
+ clinical_drug_form TEXT NOT NULL,
+ disposition TEXT NOT NULL,
+ PRIMARY KEY (clinical_drug_form, disposition),
FOREIGN KEY (clinical_drug_form) REFERENCES clinical_drug_form(curie),
FOREIGN KEY (disposition) REFERENCES disposition(curie)
);
CREATE TABLE clinical_drug (
curie TEXT PRIMARY KEY,
- label TEXT, -- UNIQUE,
- clinical_drug_form TEXT,
- rxcui INTEGER,
+ label TEXT NOT NULL, -- UNIQUE,
+ clinical_drug_form TEXT NOT NULL,
+ rxcui INTEGER NOT NULL,
FOREIGN KEY (clinical_drug_form) REFERENCES clinical_drug_form(curie),
FOREIGN KEY (rxcui) REFERENCES rxcui(rxcui)
);
CREATE TABLE clinical_drug_strength (
- clinical_drug TEXT,
- ingredient TEXT,
- strength TEXT,
- unit TEXT,
+ clinical_drug TEXT NOT NULL,
+ ingredient TEXT NOT NULL,
+ strength TEXT NOT NULL,
+ unit TEXT NOT NULL,
+ -- WARN: There are some clinical drugs in RxNorm
+ -- with the same ingredient but multiple strengths.
+ PRIMARY KEY (clinical_drug, ingredient, strength, unit),
FOREIGN KEY (clinical_drug) REFERENCES clinical_drug(curie),
FOREIGN KEY (ingredient) REFERENCES ingredient(curie)
);
CREATE TABLE branded_drug (
curie TEXT PRIMARY KEY,
- label TEXT, -- UNIQUE,
- clinical_drug TEXT,
- rxcui INTEGER,
+ label TEXT NOT NULL, -- UNIQUE,
+ clinical_drug TEXT NOT NULL,
+ rxcui INTEGER NOT NULL,
FOREIGN KEY (clinical_drug) REFERENCES clinical_drug(curie),
FOREIGN KEY (rxcui) REFERENCES rxcui(rxcui)
);
CREATE TABLE branded_drug_excipient (
- branded_drug TEXT,
- ingredient TEXT,
+ branded_drug TEXT NOT NULL,
+ ingredient TEXT NOT NULL,
+ PRIMARY KEY (branded_drug, ingredient),
FOREIGN KEY (branded_drug) REFERENCES branded_drug(curie),
FOREIGN KEY (ingredient) REFERENCES ingredient(curie)
);
CREATE TABLE ndc_branded_drug (
curie TEXT PRIMARY KEY,
- ndc TEXT,
- branded_drug TEXT,
+ ndc TEXT UNIQUE NOT NULL,
+ branded_drug TEXT NOT NULL,
FOREIGN KEY (branded_drug) REFERENCES branded_drug(curie)
);
CREATE TABLE ndc_clinical_drug (
curie TEXT PRIMARY KEY,
- ndc TEXT,
- clinical_drug TEXT,
+ ndc TEXT UNIQUE NOT NULL,
+ clinical_drug TEXT NOT NULL,
FOREIGN KEY (clinical_drug) REFERENCES clinical_drug(curie)
);
+CREATE TABLE obsolete (
+ curie TEXT PRIMARY KEY NOT NULL,
+ label TEXT NOT NULL, -- UNIQUE,
+ type TEXT NOT NULL,
+ replaced_by TEXT
+);
-- 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 );
-INSERT INTO current_dron_id VALUES (1000000); -- TODO: check this!
+-- INSERT INTO current_dron_id VALUES (1003000);
-- Then create a trigger for each row where a CURIE can be assigned:
-- When a row is inserted into the table,
diff --git a/src/scripts/index-dron-tables.sql b/src/scripts/index-dron-tables.sql
new file mode 100644
index 0000000..4719f9b
--- /dev/null
+++ b/src/scripts/index-dron-tables.sql
@@ -0,0 +1,36 @@
+-- Index main DrOn tables.
+
+CREATE INDEX IF NOT EXISTS idx_ingredient_curie ON ingredient(curie);
+CREATE INDEX IF NOT EXISTS idx_ingredient_label ON ingredient(label);
+CREATE INDEX IF NOT EXISTS idx_ingredient_rxcui ON ingredient(rxcui);
+
+CREATE INDEX IF NOT EXISTS idx_clinical_drug_form_curie ON clinical_drug_form(curie);
+CREATE INDEX IF NOT EXISTS idx_clinical_drug_form_label ON clinical_drug_form(label);
+CREATE INDEX IF NOT EXISTS idx_clinical_drug_form_rxcui ON clinical_drug_form(rxcui);
+
+CREATE INDEX IF NOT EXISTS idx_clinical_drug_form_ingredient_clinical_drug_form ON clinical_drug_form_ingredient(clinical_drug_form);
+CREATE INDEX IF NOT EXISTS idx_clinical_drug_form_ingredient_ingredient ON clinical_drug_form_ingredient(ingredient);
+
+CREATE INDEX IF NOT EXISTS idx_clinical_drug_curie ON clinical_drug(curie);
+CREATE INDEX IF NOT EXISTS idx_clinical_drug_label ON clinical_drug(label);
+CREATE INDEX IF NOT EXISTS idx_clinical_drug_rxcui ON clinical_drug(rxcui);
+
+CREATE INDEX IF NOT EXISTS idx_clinical_drug_strength_clinical_drug ON clinical_drug_strength(clinical_drug);
+CREATE INDEX IF NOT EXISTS idx_clinical_drug_strength_ingredient ON clinical_drug_strength(ingredient);
+
+CREATE INDEX IF NOT EXISTS idx_branded_drug_curie ON branded_drug(curie);
+CREATE INDEX IF NOT EXISTS idx_branded_drug_label ON branded_drug(label);
+CREATE INDEX IF NOT EXISTS idx_branded_drug_rxcui ON branded_drug(rxcui);
+
+CREATE INDEX IF NOT EXISTS idx_branded_drug_excipient_branded_drug ON branded_drug_excipient(branded_drug);
+CREATE INDEX IF NOT EXISTS idx_branded_drug_excipient_ingredient ON branded_drug_excipient(ingredient);
+
+CREATE INDEX IF NOT EXISTS idx_ndc_clinical_drug_curie ON ndc_clinical_drug(curie);
+CREATE INDEX IF NOT EXISTS idx_ndc_clinical_drug_ndc ON ndc_clinical_drug(ndc);
+CREATE INDEX IF NOT EXISTS idx_ndc_clinical_drug_clinical_drug ON ndc_clinical_drug(clinical_drug);
+
+CREATE INDEX IF NOT EXISTS idx_ndc_branded_drug_curie ON ndc_branded_drug(curie);
+CREATE INDEX IF NOT EXISTS idx_ndc_branded_drug_ndc ON ndc_branded_drug(ndc);
+CREATE INDEX IF NOT EXISTS idx_ndc_branded_drug_branded_drug ON ndc_branded_drug(branded_drug);
+
+ANALYZE;
diff --git a/src/scripts/load-dron-tables.sql b/src/scripts/load-dron-tables.sql
index 547e4ac..300a520 100644
--- a/src/scripts/load-dron-tables.sql
+++ b/src/scripts/load-dron-tables.sql
@@ -18,3 +18,29 @@ PRAGMA foreign_keys = ON;
.import --skip 1 ../templates/branded_drug_excipient.tsv branded_drug_excipient
.import --skip 1 ../templates/ndc_branded_drug.tsv ndc_branded_drug
.import --skip 1 ../templates/ndc_clinical_drug.tsv ndc_clinical_drug
+.import --skip 1 ../templates/obsolete.tsv obsolete
+
+-- Set current_dron_id.
+DELETE FROM current_dron_id;
+WITH curie AS (
+ SELECT curie FROM ingredient
+ UNION ALL
+ SELECT curie FROM clinical_drug_form
+ UNION ALL
+ SELECT curie FROM clinical_drug
+ UNION ALL
+ SELECT curie FROM branded_drug
+ UNION ALL
+ SELECT curie FROM ndc_clinical_drug
+ UNION ALL
+ SELECT curie FROM ndc_branded_drug
+ UNION ALL
+ SELECT curie FROM obsolete
+),
+max_curie AS (
+ SELECT MAX(CURIE) AS curie
+ FROM curie
+)
+INSERT INTO current_dron_id
+SELECT CAST(REPLACE(curie, 'DRON:', '') AS INTEGER) AS id
+FROM max_curie;
diff --git a/src/scripts/obsolete-dron-duplicates.sh b/src/scripts/obsolete-dron-duplicates.sh
new file mode 100755
index 0000000..4d8846f
--- /dev/null
+++ b/src/scripts/obsolete-dron-duplicates.sh
@@ -0,0 +1,28 @@
+#!/bin/sh
+#
+# Add DRON duplicates to obsolete.tsv,
+# keeping the term with the lower ID number.
+
+fail() {
+ echo "ERROR: " "$@"
+ exit 1
+}
+
+ROOT=$(git rev-parse --show-toplevel) || fail "Not a git repository"
+DIR="${ROOT}/src/ontology"
+SCRIPTSDIR="${ROOT}/src/scripts"
+TEMPLATEDIR="${ROOT}/src/templates"
+DB="${DIR}/tmp/dron.db"
+
+# Load template TSVs into SQLite.
+cd "${DIR}" || fail "Could not cd to ${DIR}"
+make tmp/dron.db || fail "Could not make tmp/dron.db"
+
+# Find DRON ingredients matching ChEBI labels.
+sqlite3 < "${SCRIPTSDIR}/obsolete-dron-duplicates.sql" \
+|| fail "Could not run query for duplicates"
+
+# Save obsolete.tsv.
+cd "${TEMPLATEDIR}" \
+&& sqlite3 "${DB}" < "${SCRIPTSDIR}/save-dron-tables.sql" \
+|| fail "Could not save updated obsolete.tsv"
diff --git a/src/scripts/obsolete-dron-duplicates.sql b/src/scripts/obsolete-dron-duplicates.sql
new file mode 100644
index 0000000..e0142b3
--- /dev/null
+++ b/src/scripts/obsolete-dron-duplicates.sql
@@ -0,0 +1,101 @@
+-- Add DRON duplicates to obsolete.tsv,
+-- with identical 'label' and 'rxcui',
+-- keeping the term with the lower ID number.
+
+ATTACH 'tmp/dron.db' AS dron;
+
+DROP TABLE IF EXISTS duplicates_to_keep;
+CREATE TABLE duplicates_to_keep (
+ curie TEXT PRIMARY KEY,
+ label TEXT UNIQUE,
+ rxcui INTEGER
+);
+
+INSERT OR IGNORE INTO duplicates_to_keep
+SELECT
+ min(curie) AS curie,
+ label AS label,
+ rxcui AS rxcui
+FROM dron.ingredient
+GROUP BY label, rxcui
+HAVING COUNT(*) > 1;
+
+INSERT OR IGNORE INTO duplicates_to_keep
+SELECT
+ min(curie) AS curie,
+ label AS label,
+ rxcui AS rxcui
+FROM dron.clinical_drug_form
+GROUP BY label, rxcui
+HAVING COUNT(*) > 1;
+
+INSERT OR IGNORE INTO duplicates_to_keep
+SELECT
+ min(curie) AS curie,
+ label AS label,
+ rxcui AS rxcui
+FROM dron.clinical_drug
+GROUP BY label, rxcui
+HAVING COUNT(*) > 1;
+
+INSERT OR IGNORE INTO duplicates_to_keep
+SELECT
+ min(curie) AS curie,
+ label AS label,
+ rxcui AS rxcui
+FROM dron.branded_drug
+GROUP BY label, rxcui
+HAVING COUNT(*) > 1;
+
+CREATE INDEX idx_duplicate_label ON duplicates_to_keep(label);
+CREATE INDEX idx_duplicate_rxcui ON duplicates_to_keep(rxcui);
+
+INSERT OR IGNORE INTO dron.obsolete
+SELECT
+ i.curie AS curie,
+ 'obsolete ' || i.label AS label,
+ 'owl:Class' AS type,
+ d.curie AS replaced_by
+FROM dron.ingredient AS i
+JOIN duplicates_to_keep AS d
+WHERE i.label = d.label
+ AND i.rxcui = d.rxcui
+ AND i.curie NOT IN (SELECT curie FROM duplicates_to_keep);
+
+INSERT OR IGNORE INTO dron.obsolete
+SELECT
+ i.curie AS curie,
+ 'obsolete ' || i.label AS label,
+ 'owl:Class' AS type,
+ d.curie AS replaced_by
+FROM dron.clinical_drug_form AS i
+JOIN duplicates_to_keep AS d
+WHERE i.label = d.label
+ AND i.rxcui = d.rxcui
+ AND i.curie NOT IN (SELECT curie FROM duplicates_to_keep);
+
+INSERT OR IGNORE INTO dron.obsolete
+SELECT
+ i.curie AS curie,
+ 'obsolete ' || i.label AS label,
+ 'owl:Class' AS type,
+ d.curie AS replaced_by
+FROM dron.clinical_drug AS i
+JOIN duplicates_to_keep AS d
+WHERE i.label = d.label
+ AND i.rxcui = d.rxcui
+ AND i.curie NOT IN (SELECT curie FROM duplicates_to_keep);
+
+INSERT OR IGNORE INTO dron.obsolete
+SELECT
+ i.curie AS curie,
+ 'obsolete ' || i.label AS label,
+ 'owl:Class' AS type,
+ d.curie AS replaced_by
+FROM dron.branded_drug AS i
+JOIN duplicates_to_keep AS d
+WHERE i.label = d.label
+ AND i.rxcui = d.rxcui
+ AND i.curie NOT IN (SELECT curie FROM duplicates_to_keep);
+
+DROP TABLE duplicates_to_keep;
diff --git a/src/scripts/obsolete-dron-ingredients.sh b/src/scripts/obsolete-dron-ingredients.sh
new file mode 100755
index 0000000..91d2739
--- /dev/null
+++ b/src/scripts/obsolete-dron-ingredients.sh
@@ -0,0 +1,29 @@
+#!/bin/sh
+#
+# Add DRON ingredients to obsolete.tsv
+# if they match ChEBI labels.
+
+fail() {
+ echo "ERROR: " "$@"
+ exit 1
+}
+
+ROOT=$(git rev-parse --show-toplevel) || fail "Not a git repository"
+DIR="${ROOT}/src/ontology"
+SCRIPTSDIR="${ROOT}/src/scripts"
+TEMPLATEDIR="${ROOT}/src/templates"
+DB="${DIR}/tmp/dron.db"
+
+# Load template TSVs into SQLite.
+cd "${DIR}" || fail "Could not cd to ${DIR}"
+make tmp/dron.db || fail "Could not make tmp/dron.db"
+make tmp/chebi.db || fail "Could not make tmp/chebi.db"
+
+# Find DRON ingredients matching ChEBI labels.
+sqlite3 "${DB}" < "${SCRIPTSDIR}/obsolete-dron-ingredients.sql" \
+|| fail "Could not run query for ingredients"
+
+# Save obsolete.tsv.
+cd "${TEMPLATEDIR}" \
+&& sqlite3 "${DB}" < "${SCRIPTSDIR}/save-dron-tables.sql" \
+|| fail "Could not save updated obsolete.tsv"
diff --git a/src/scripts/obsolete-dron-ingredients.sql b/src/scripts/obsolete-dron-ingredients.sql
new file mode 100644
index 0000000..499edfd
--- /dev/null
+++ b/src/scripts/obsolete-dron-ingredients.sql
@@ -0,0 +1,16 @@
+-- Add DRON ingredients to obsolete.tsv
+-- if they match ChEBI labels.
+
+ATTACH 'tmp/dron.db' AS dron;
+ATTACH 'tmp/chebi.db' AS chebi;
+
+CREATE INDEX IF NOT EXISTS dron.idx_ingredient_label ON ingredient(label);
+INSERT OR IGNORE INTO dron.obsolete
+SELECT
+ i.curie AS curie,
+ 'obsolete ' || i.label AS label,
+ 'owl:Class' AS type,
+ c.subject AS replaced_by
+FROM dron.ingredient AS i
+JOIN chebi.label AS c ON c.label = i.label
+WHERE i.curie LIKE 'DRON:%';
diff --git a/src/scripts/obsolete-terms.sh b/src/scripts/obsolete-terms.sh
new file mode 100755
index 0000000..1897eb0
--- /dev/null
+++ b/src/scripts/obsolete-terms.sh
@@ -0,0 +1,47 @@
+#!/bin/sh
+#
+# Obsolete a DRON term and replace it with another term.
+
+fail() {
+ echo "ERROR: " "$@"
+ exit 1
+}
+
+ROOT=$(git rev-parse --show-toplevel) || fail "Not a git repository"
+DIR="${ROOT}/src/ontology"
+SCRIPTSDIR="${ROOT}/src/scripts"
+TEMPLATEDIR="${ROOT}/src/templates"
+DB="${DIR}/tmp/dron.db"
+
+# Replace one term ID with another ID throughout.
+replace() {
+ OBSOLETE="$1"
+ REPLACEMENT="$2"
+ if [ -n "${REPLACEMENT}" ]; then
+ < "${SCRIPTSDIR}/obsolete-terms.sql" \
+ sed "s/OBSOLETE/${OBSOLETE}/g" \
+ | sed "s/REPLACEMENT/${REPLACEMENT}/g" \
+ | sqlite3 "${DB}" \
+ > /dev/null \
+ || fail "Could not obsolete ${OBSOLETE}, replaced by ${REPLACEMENT}"
+ fi
+}
+
+# Load template TSVs into SQLite.
+cd "${DIR}" || fail "Could not cd to ${DIR}"
+make tmp/dron.db || fail "Could not make ${DB}"
+
+COUNT=$(wc -l < "$TEMPLATEDIR/obsolete.tsv")
+echo "Attempting to replace ${COUNT} obsolete terms..."
+
+# Iterate over the rows of obsolete.tsv and replace.
+tail -n+2 "${TEMPLATEDIR}/obsolete.tsv" \
+| cut -f1,4 \
+| while read -r p; do
+ replace $p
+done
+
+# Save templates TSVs.
+cd "${TEMPLATEDIR}" \
+&& sqlite3 "${DB}" <