Obsolete and replace terms

src/ontology/catalog-v001.xml

@@ -29,6 +29,7 @@
 
   <!--  <uri name="http://purl.obolibrary.org/obo/dron/dron-upper.owl" uri="components/dron-upper.owl"/>-->
 
-
+  <uri name="http://purl.obolibrary.org/obo/dron/dron-obsolete.owl" uri="components/dron-obsolete.owl"/>
+
 </group>
-</catalog>
+</catalog>

src/ontology/dron-edit.owl

@@ -12,6 +12,7 @@ Ontology(<http://purl.obolibrary.org/obo/dron.owl>
 Import(<http://purl.obolibrary.org/obo/dron/dron-ingredient.owl>)
 Import(<http://purl.obolibrary.org/obo/dron/dron-ndc.owl>)
 Import(<http://purl.obolibrary.org/obo/dron/dron-rxnorm.owl>)
+Import(<http://purl.obolibrary.org/obo/dron/dron-obsolete.owl>)
 Import(<http://purl.obolibrary.org/obo/dron/imports/apollo_sv_import.owl>)
 Import(<http://purl.obolibrary.org/obo/dron/imports/bfo_import.owl>)
 Import(<http://purl.obolibrary.org/obo/dron/imports/chebi_import.owl>)
@@ -2160,4 +2161,4 @@ AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000412> <http://purl.ob
 
 
 AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000117> <http://purl.obolibrary.org/obo/DRON_00723856> "ciara lusnia")
-)
+)

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 [email protected] && mv [email protected] $@
@@ -61,13 +61,18 @@ update-labels: $(TMPDIR)/dron.db $(TMPDIR)/chebi.db $(TMPDIR)/rxnorm.db $(SCRIPT
 	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
 	$(eval DB=$@)
 	rm -f $@
 	$(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 +86,7 @@ $(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 +104,19 @@ $(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 +150,4 @@ $(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

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 != '';

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';

src/scripts/create-dron-tables.sql

@@ -94,6 +94,12 @@ CREATE TABLE ndc_clinical_drug (
     FOREIGN KEY (clinical_drug) REFERENCES clinical_drug(curie)
 );
 
+CREATE TABLE obsolete (
+    curie TEXT PRIMARY KEY,
+    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.

src/scripts/load-dron-tables.sql

@@ -18,3 +18,4 @@ 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

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"

src/scripts/obsolete-dron-ingredients.sql

@@ -0,0 +1,18 @@
+ATTACH 'tmp/dron.db' AS dron;
+ATTACH 'tmp/chebi.db' AS chebi;
+
+CREATE INDEX IF NOT EXISTS dron.idx_ingredient_label ON ingredient(label);
+WITH labels AS (
+    SELECT subject, object AS label
+    FROM chebi.chebi
+    WHERE predicate = 'rdfs:label'
+)
+INSERT OR IGNORE INTO dron.obsolete
+SELECT
+    i.curie AS curie,
+    'obsolete ' || i.label AS label,
+    'owl:Class' AS type,
+    l.subject AS replaced_by
+FROM dron.ingredient AS i
+JOIN labels AS l ON l.label = i.label
+WHERE i.curie LIKE 'DRON:%';

src/scripts/obsolete-terms.sh

@@ -0,0 +1,43 @@
+#!/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}" \
+    || fail "Could not obsolete ${OBSOLETE}"
+  fi
+}
+
+# Load template TSVs into SQLite.
+cd "${DIR}" || fail "Could not cd to ${DIR}"
+make tmp/dron.db || fail "Could not make ${DB}"
+
+# Iterate over the rows of obsolete.tsv and replace.
+tail -n+2 "${TEMPLATEDIR}/obsolete.tsv" \
+| cut -f1,4 \
+| while read -r p; do
+  replace $p
+done
+
+# Save templates TSVs.
+cd "${TEMPLATEDIR}" \
+&& sqlite3 "${DB}" < "${SCRIPTSDIR}/save-dron-tables.sql" \
+|| fail "Could not save updated templates"

src/scripts/obsolete-terms.sql

@@ -0,0 +1,110 @@
+PRAGMA foreign_keys = ON;
+
+BEGIN TRANSACTION;
+
+-- obsolete ingredient
+
+INSERT OR IGNORE INTO ingredient
+SELECT
+    'REPLACEMENT' AS curie,
+    label AS label,
+    rxcui AS rxcui
+FROM ingredient
+WHERE curie = 'OBSOLETE';
+
+UPDATE ingredient_disposition
+SET ingredient = 'REPLACEMENT'
+WHERE ingredient = 'OBSOLETE';
+
+UPDATE clinical_drug_form_ingredient
+SET ingredient = 'REPLACEMENT'
+WHERE ingredient = 'OBSOLETE';
+
+UPDATE clinical_drug_strength
+SET ingredient = 'REPLACEMENT'
+WHERE ingredient = 'OBSOLETE';
+
+UPDATE branded_drug_excipient
+SET ingredient = 'REPLACEMENT'
+WHERE ingredient = 'OBSOLETE';
+
+DELETE FROM ingredient
+WHERE curie = 'OBSOLETE';
+
+-- obsolete clinical_drug_form
+
+INSERT OR IGNORE INTO clinical_drug_form
+SELECT
+    'REPLACEMENT' AS curie,
+    label AS label,
+    parent AS parent,
+    rxcui AS rxcui
+FROM clinical_drug_form
+WHERE curie = 'OBSOLETE';
+
+UPDATE clinical_drug_form_ingredient
+SET clinical_drug_form = 'REPLACEMENT'
+WHERE clinical_drug_form = 'OBSOLETE';
+
+UPDATE clinical_drug_form_disposition
+SET clinical_drug_form = 'REPLACEMENT'
+WHERE clinical_drug_form = 'OBSOLETE';
+
+UPDATE clinical_drug
+SET clinical_drug_form = 'REPLACEMENT'
+WHERE clinical_drug_form = 'OBSOLETE';
+
+DELETE FROM clinical_drug_form
+WHERE curie = 'OBSOLETE';
+
+-- obsolete clinical_drug
+
+INSERT OR IGNORE INTO clinical_drug
+SELECT
+    'REPLACEMENT' AS curie,
+    label AS label,
+    clinical_drug_form AS clinical_drug_form,
+    rxcui AS rxcui
+FROM clinical_drug
+WHERE curie = 'OBSOLETE';
+
+UPDATE clinical_drug_strength
+SET clinical_drug = 'REPLACEMENT'
+WHERE clinical_drug = 'OBSOLETE';
+
+UPDATE branded_drug
+SET clinical_drug = 'REPLACEMENT'
+WHERE clinical_drug = 'OBSOLETE';
+
+UPDATE ndc_clinical_drug
+SET clinical_drug = 'REPLACEMENT'
+WHERE clinical_drug = 'OBSOLETE';
+
+DELETE FROM clinical_drug
+WHERE curie = 'OBSOLETE';
+
+-- obsolete branded_drug
+
+INSERT OR IGNORE INTO branded_drug
+SELECT
+    'REPLACEMENT' AS curie,
+    label AS label,
+    clinical_drug AS clinical_drug,
+    rxcui AS rxcui
+FROM branded_drug
+WHERE curie = 'OBSOLETE';
+
+UPDATE branded_drug_excipient
+SET branded_drug = 'REPLACEMENT'
+WHERE branded_drug = 'OBSOLETE';
+
+UPDATE ndc_branded_drug
+SET branded_drug = 'REPLACEMENT'
+WHERE branded_drug = 'OBSOLETE';
+
+DELETE FROM branded_drug
+WHERE curie = 'OBSOLETE';
+
+-- done
+
+COMMIT;