From fd5a294d089a5fdd92de5b9bdfc57c423c4dc7e0 Mon Sep 17 00:00:00 2001
From: cmungall <cjm@berkeleybop.org>
Date: Sat, 17 Dec 2022 12:35:11 -0800
Subject: [PATCH 1/2] node identifiers

---
 Makefile                                      |  28 +-
 ontologies.Makefile                           |  48 +-
 src/semsql/builder/build.Makefile             |   2 +-
 src/semsql/builder/prefixes/obo_prefixes.csv  | 762 +++++++++++++++++
 src/semsql/builder/prefixes/obo_prefixes.db   | Bin 110592 -> 204800 bytes
 src/semsql/builder/prefixes/prefixes.csv      | 767 ++++++++++++++++++
 .../builder/prefixes/prefixes_local.csv       |   5 +
 src/semsql/builder/registry/ontologies.yaml   |  21 +
 src/semsql/builder/sql_schema/rdf.sql         |  17 +
 src/semsql/builder/sql_schema/semsql.sql      |  17 +
 src/semsql/linkml/rdf.yaml                    |  21 +
 src/semsql/linkml/semsql.yaml                 |   2 +-
 src/semsql/sqla/omo.py                        |  96 ++-
 src/semsql/sqla/owl.py                        |  13 +
 src/semsql/sqla/rdf.py                        |  13 +
 src/semsql/sqla/semsql.py                     |  68 ++
 tests/inputs/go-nucleus.db                    | Bin 1847296 -> 1847296 bytes
 tests/test_orm/test_basic_sqla.py             |  14 +-
 18 files changed, 1861 insertions(+), 33 deletions(-)

diff --git a/Makefile b/Makefile
index b47c99d..2062528 100644
--- a/Makefile
+++ b/Makefile
@@ -22,8 +22,11 @@ STAGED_ONTOLOGIES = $(patsubst %, stage/%.db.gz, $(ALL_ONTS))
 TEST_ONTOLOGIES = go-nucleus robot-example
 
 
+include ontologies.Makefile
+
 all: build_all stage_all
-build_all: $(patsubst %,all-%,$(ALL_ONTS))
+build_all: $(patsubst %, all-%, $(ALL_ONTS))
+	echo building $(ALL_ONTS)
 stage_all: $(STAGED_ONTOLOGIES)
 	echo done $(STAGED_ONTOLOGIES)
 
@@ -79,17 +82,17 @@ realclean-%:
 
 build_prefixes: $(PREFIX_DIR)/prefixes.csv
 
-$(PREFIX_DIR)/obo_prefixes.owl:
-	robot convert -I http://purl.obolibrary.org/meta/obo_prefixes.ttl -o $@
+#$(PREFIX_DIR)/obo_prefixes.owl:
+#	robot convert -I http://purl.obolibrary.org/meta/obo_prefixes.ttl -o $@
 
-$(PREFIX_DIR)/obo_prefixes.db: $(PREFIX_DIR)/obo_prefixes.owl
-	sqlite3 $@ < $(PREFIX_DIR)/prefix_ddl.sql && ./bin/rdftab $@ < $<
+#$(PREFIX_DIR)/obo_prefixes.db: $(PREFIX_DIR)/obo_prefixes.owl
+#	sqlite3 $@ < $(PREFIX_DIR)/prefix_ddl.sql && ./bin/rdftab $@ < $<
 
-$(PREFIX_DIR)/obo_prefixes.csv: $(PREFIX_DIR)/obo_prefixes.db
-	sqlite3 $< -cmd ".separator ','" "SELECT p.value AS prefix, ns.value AS base FROM statements AS p JOIN statements AS ns ON (p.subject=ns.subject) WHERE p.predicate='<http://www.w3.org/ns/shacl#prefix>' AND ns.predicate='<http://www.w3.org/ns/shacl#namespace>'" > $@
+#$(PREFIX_DIR)/obo_prefixes.csv: $(PREFIX_DIR)/obo_prefixes.db
+#	sqlite3 $< -cmd ".separator ','" "SELECT p.value AS prefix, ns.value AS base FROM statements AS p JOIN statements AS ns ON (p.subject=ns.subject) WHERE p.predicate='<http://www.w3.org/ns/shacl#prefix>' AND ns.predicate='<http://www.w3.org/ns/shacl#namespace>'" > $@
 
-$(PREFIX_DIR)/prefixes.csv: $(PREFIX_DIR)/prefixes_curated.csv $(PREFIX_DIR)/obo_prefixes.csv
-	cat $^ > $@
+#$(PREFIX_DIR)/prefixes.csv: $(PREFIX_DIR)/prefixes_curated.csv $(PREFIX_DIR)/obo_prefixes.csv#
+#	cat $^ > $@
 
 
 # ---
@@ -133,13 +136,6 @@ reports/%.problems.tsv: db/%.db target/%.views
 STAMP:
 	touch $@
 
-db/reactome-Homo-sapiens.owl: download/reactome-biopax.zip db/biopax.owl
-	unzip -p $< Homo_sapiens.owl > $@.tmp &&\
-	robot merge -i $@.tmp  -i db/biopax.owl -o $@
-
-download/reactome-biopax.zip:
-	curl -L -s https://reactome.org/download/current/biopax.zip > $@
-
 ## Additional ontologies
 
 src/semsql/builder/registry/registry_schema.py: src/semsql/builder/registry/registry_schema.yaml
diff --git a/ontologies.Makefile b/ontologies.Makefile
index ff655a3..a0c1c0c 100644
--- a/ontologies.Makefile
+++ b/ontologies.Makefile
@@ -28,7 +28,7 @@ download/maxo.owl: STAMP
 .PRECIOUS: download/maxo.owl
 
 db/maxo.owl: download/maxo.owl
-	robot relax -i $< merge -o $@
+	robot relax -i $< merge reason -r structural -o $@
 
 
 download/foodon.owl: STAMP
@@ -372,6 +372,50 @@ db/uniprot.owl: download/uniprot.owl
 	cp $< $@
 
 
+download/rhea.owl: STAMP
+	curl -L -s https://github.com/biopragmatics/obo-db-ingest/raw/main/export/rhea/122/rhea.owl.gz | gzip -dc > $@.tmp
+	sha256sum -b $@.tmp > $@.sha256
+	mv $@.tmp $@
+
+.PRECIOUS: download/rhea.owl
+
+db/rhea.owl: download/rhea.owl
+	cp $< $@
+
+
+download/drugbank.owl: STAMP
+	curl -L -s https://github.com/biopragmatics/obo-db-ingest/raw/main/export/drugbank/5.1.9/drugbank.owl.gz | gzip -dc > $@.tmp
+	sha256sum -b $@.tmp > $@.sha256
+	mv $@.tmp $@
+
+.PRECIOUS: download/drugbank.owl
+
+db/drugbank.owl: download/drugbank.owl
+	cp $< $@
+
+
+download/drugcentral.owl: STAMP
+	curl -L -s https://github.com/biopragmatics/obo-db-ingest/raw/main/export/drugcentral.owl.gz | gzip -dc > $@.tmp
+	sha256sum -b $@.tmp > $@.sha256
+	mv $@.tmp $@
+
+.PRECIOUS: download/drugcentral.owl
+
+db/drugcentral.owl: download/drugcentral.owl
+	cp $< $@
+
+
+download/complexportal.owl: STAMP
+	curl -L -s https://github.com/biopragmatics/obo-db-ingest/raw/main/export/complexportal/2022-02-03/complexportal.owl.gz | gzip -dc > $@.tmp
+	sha256sum -b $@.tmp > $@.sha256
+	mv $@.tmp $@
+
+.PRECIOUS: download/complexportal.owl
+
+db/complexportal.owl: download/complexportal.owl
+	cp $< $@
+
+
 download/%.owl: STAMP
 	curl -L -s http://purl.obolibrary.org/obo/$*.owl > $@.tmp
 	sha256sum -b $@.tmp > $@.sha256
@@ -382,4 +426,4 @@ download/%.owl: STAMP
 db/%.owl: download/%.owl
 	robot merge -i $< -o $@
 
-EXTRA_ONTOLOGIES = chiro ncit maxo foodon chebiplus msio phenio comploinc bero aio reacto go go-lego bao orcid cpont biolink biopax enanomapper mlo ito reactome-Homo-sapiens efo edam sweetAll lov schema-dot-org cosmo co_324 hgnc.genegroup hgnc dictybase eccode uniprot
+EXTRA_ONTOLOGIES = chiro ncit maxo foodon chebiplus msio phenio comploinc bero aio reacto go go-lego bao orcid cpont biolink biopax enanomapper mlo ito reactome-Homo-sapiens efo edam sweetAll lov schema-dot-org cosmo co_324 hgnc.genegroup hgnc dictybase eccode uniprot rhea drugbank drugcentral complexportal
diff --git a/src/semsql/builder/build.Makefile b/src/semsql/builder/build.Makefile
index 0d5078f..0af149e 100644
--- a/src/semsql/builder/build.Makefile
+++ b/src/semsql/builder/build.Makefile
@@ -95,7 +95,7 @@ $(PREFIX_DIR)/obo_prefixes.owl:
 	robot convert -I http://purl.obolibrary.org/meta/obo_prefixes.ttl -o $@
 
 $(PREFIX_DIR)/obo_prefixes.db: $(PREFIX_DIR)/obo_prefixes.owl
-	sqlite3 $@ < $(PREFIX_DIR)/prefix_ddl.sql && ./bin/rdftab $@ < $<
+	sqlite3 $@ < $(PREFIX_DIR)/prefix_ddl.sql && rdftab $@ < $<
 
 $(PREFIX_DIR)/obo_prefixes.csv: $(PREFIX_DIR)/obo_prefixes.db
 	sqlite3 $< -cmd ".separator ','" "SELECT p.value AS prefix, ns.value AS base FROM statements AS p JOIN statements AS ns ON (p.subject=ns.subject) WHERE p.predicate='<http://www.w3.org/ns/shacl#prefix>' AND ns.predicate='<http://www.w3.org/ns/shacl#namespace>'" > $@
diff --git a/src/semsql/builder/prefixes/obo_prefixes.csv b/src/semsql/builder/prefixes/obo_prefixes.csv
index 46b0639..e71567d 100644
--- a/src/semsql/builder/prefixes/obo_prefixes.csv
+++ b/src/semsql/builder/prefixes/obo_prefixes.csv
@@ -1,254 +1,1016 @@
 RBO,http://purl.obolibrary.org/obo/RBO_
+RBO,http://purl.obolibrary.org/obo/RBO_
+CLYH,http://purl.obolibrary.org/obo/CLYH_
+CLYH,http://purl.obolibrary.org/obo/CLYH_
+RO,http://purl.obolibrary.org/obo/RO_
+RO,http://purl.obolibrary.org/obo/RO_
+CMO,http://purl.obolibrary.org/obo/CMO_
+CMO,http://purl.obolibrary.org/obo/CMO_
+RS,http://purl.obolibrary.org/obo/RS_
+RS,http://purl.obolibrary.org/obo/RS_
+COB,http://purl.obolibrary.org/obo/COB_
+COB,http://purl.obolibrary.org/obo/COB_
+RXNO,http://purl.obolibrary.org/obo/RXNO_
+RXNO,http://purl.obolibrary.org/obo/RXNO_
+COLAO,http://purl.obolibrary.org/obo/COLAO_
+COLAO,http://purl.obolibrary.org/obo/COLAO_
+PSDO,http://purl.obolibrary.org/obo/PSDO_
+PSDO,http://purl.obolibrary.org/obo/PSDO_
+PSO,http://purl.obolibrary.org/obo/PSO_
+PSO,http://purl.obolibrary.org/obo/PSO_
+CLAO,http://purl.obolibrary.org/obo/CLAO_
+CLAO,http://purl.obolibrary.org/obo/CLAO_
+PW,http://purl.obolibrary.org/obo/PW_
+PW,http://purl.obolibrary.org/obo/PW_
+CLO,http://purl.obolibrary.org/obo/CLO_
+CLO,http://purl.obolibrary.org/obo/CLO_
+SEPIO,http://purl.obolibrary.org/obo/SEPIO_
+SEPIO,http://purl.obolibrary.org/obo/SEPIO_
+CRO,http://purl.obolibrary.org/obo/CRO_
+CRO,http://purl.obolibrary.org/obo/CRO_
+SO,http://purl.obolibrary.org/obo/SO_
+SO,http://purl.obolibrary.org/obo/SO_
+CTENO,http://purl.obolibrary.org/obo/CTENO_
+CTENO,http://purl.obolibrary.org/obo/CTENO_
+SPD,http://purl.obolibrary.org/obo/SPD_
+SPD,http://purl.obolibrary.org/obo/SPD_
+CTO,http://purl.obolibrary.org/obo/CTO_
+CTO,http://purl.obolibrary.org/obo/CTO_
+CVDO,http://purl.obolibrary.org/obo/CVDO_
+CVDO,http://purl.obolibrary.org/obo/CVDO_
+DISDRIV,http://purl.obolibrary.org/obo/DISDRIV_
+DISDRIV,http://purl.obolibrary.org/obo/DISDRIV_
+DOID,http://purl.obolibrary.org/obo/DOID_
+DOID,http://purl.obolibrary.org/obo/DOID_
+FBcv,http://purl.obolibrary.org/obo/FBcv_
+FBcv,http://purl.obolibrary.org/obo/FBcv_
+DRON,http://purl.obolibrary.org/obo/DRON_
+DRON,http://purl.obolibrary.org/obo/DRON_
+DDANAT,http://purl.obolibrary.org/obo/DDANAT_
+DDANAT,http://purl.obolibrary.org/obo/DDANAT_
+DDPHENO,http://purl.obolibrary.org/obo/DDPHENO_
+DDPHENO,http://purl.obolibrary.org/obo/DDPHENO_
+DIDEO,http://purl.obolibrary.org/obo/DIDEO_
+DIDEO,http://purl.obolibrary.org/obo/DIDEO_
+DUO,http://purl.obolibrary.org/obo/DUO_
+DUO,http://purl.obolibrary.org/obo/DUO_
+ECAO,http://purl.obolibrary.org/obo/ECAO_
+ECAO,http://purl.obolibrary.org/obo/ECAO_
+ECOCORE,http://purl.obolibrary.org/obo/ECOCORE_
+ECOCORE,http://purl.obolibrary.org/obo/ECOCORE_
+EUPATH,http://purl.obolibrary.org/obo/EUPATH_
+EUPATH,http://purl.obolibrary.org/obo/EUPATH_
+ExO,http://purl.obolibrary.org/obo/ExO_
+ExO,http://purl.obolibrary.org/obo/ExO_
+FAO,http://purl.obolibrary.org/obo/FAO_
+FAO,http://purl.obolibrary.org/obo/FAO_
+FBbi,http://purl.obolibrary.org/obo/FBbi_
+FBbi,http://purl.obolibrary.org/obo/FBbi_
+ECTO,http://purl.obolibrary.org/obo/ECTO_
+ECTO,http://purl.obolibrary.org/obo/ECTO_
+EMAPA,http://purl.obolibrary.org/obo/EMAPA_
+EMAPA,http://purl.obolibrary.org/obo/EMAPA_
+ENVO,http://purl.obolibrary.org/obo/ENVO_
+ENVO,http://purl.obolibrary.org/obo/ENVO_
+EPIO,http://purl.obolibrary.org/obo/EPIO_
+EPIO,http://purl.obolibrary.org/obo/EPIO_
+FBbt,http://purl.obolibrary.org/obo/FBbt_
+FBbt,http://purl.obolibrary.org/obo/FBbt_
+FBcv,http://purl.obolibrary.org/obo/FBcv_
+FBcv,http://purl.obolibrary.org/obo/FBcv_
+VSAO,http://purl.obolibrary.org/obo/VSAO_
+VSAO,http://purl.obolibrary.org/obo/VSAO_
+YPO,http://purl.obolibrary.org/obo/YPO_
+YPO,http://purl.obolibrary.org/obo/YPO_
+ZEA,http://purl.obolibrary.org/obo/ZEA_
+ZEA,http://purl.obolibrary.org/obo/ZEA_
+SWO,http://purl.obolibrary.org/obo/SWO_
+SWO,http://purl.obolibrary.org/obo/SWO_
+SYMP,http://purl.obolibrary.org/obo/SYMP_
+SYMP,http://purl.obolibrary.org/obo/SYMP_
+TAXRANK,http://purl.obolibrary.org/obo/TAXRANK_
+TAXRANK,http://purl.obolibrary.org/obo/TAXRANK_
+TO,http://purl.obolibrary.org/obo/TO_
+TO,http://purl.obolibrary.org/obo/TO_
+STATO,http://purl.obolibrary.org/obo/STATO_
+STATO,http://purl.obolibrary.org/obo/STATO_
+VT,http://purl.obolibrary.org/obo/VT_
+VT,http://purl.obolibrary.org/obo/VT_
+VTO,http://purl.obolibrary.org/obo/VTO_
+VTO,http://purl.obolibrary.org/obo/VTO_
+WBbt,http://purl.obolibrary.org/obo/WBbt_
+WBbt,http://purl.obolibrary.org/obo/WBbt_
+WBls,http://purl.obolibrary.org/obo/WBls_
+WBls,http://purl.obolibrary.org/obo/WBls_
+VBO,http://purl.obolibrary.org/obo/VBO_
+VBO,http://purl.obolibrary.org/obo/VBO_
+VO,http://purl.obolibrary.org/obo/VO_
+VO,http://purl.obolibrary.org/obo/VO_
+UPHENO,http://purl.obolibrary.org/obo/UPHENO_
+UPHENO,http://purl.obolibrary.org/obo/UPHENO_
+TRANS,http://purl.obolibrary.org/obo/TRANS_
+TRANS,http://purl.obolibrary.org/obo/TRANS_
+TTO,http://purl.obolibrary.org/obo/TTO_
+TTO,http://purl.obolibrary.org/obo/TTO_
+TXPO,http://purl.obolibrary.org/obo/TXPO_
+TXPO,http://purl.obolibrary.org/obo/TXPO_
+UO,http://purl.obolibrary.org/obo/UO_
+UO,http://purl.obolibrary.org/obo/UO_
+ZFS,http://purl.obolibrary.org/obo/ZFS_
+ZFS,http://purl.obolibrary.org/obo/ZFS_
+FLOPO,http://purl.obolibrary.org/obo/FLOPO_
+FLOPO,http://purl.obolibrary.org/obo/FLOPO_
+ZP,http://purl.obolibrary.org/obo/ZP_
+ZP,http://purl.obolibrary.org/obo/ZP_
+FOBI,http://purl.obolibrary.org/obo/FOBI_
+FOBI,http://purl.obolibrary.org/obo/FOBI_
+ECO,http://purl.obolibrary.org/obo/ECO_
+ECO,http://purl.obolibrary.org/obo/ECO_
+FOODON,http://purl.obolibrary.org/obo/FOODON_
+FOODON,http://purl.obolibrary.org/obo/FOODON_
+NOMEN,http://purl.obolibrary.org/obo/NOMEN_
+NOMEN,http://purl.obolibrary.org/obo/NOMEN_
+FOVT,http://purl.obolibrary.org/obo/FOVT_
+FOVT,http://purl.obolibrary.org/obo/FOVT_
+XPO,http://purl.obolibrary.org/obo/XPO_
+XPO,http://purl.obolibrary.org/obo/XPO_
+ZECO,http://purl.obolibrary.org/obo/ZECO_
+ZECO,http://purl.obolibrary.org/obo/ZECO_
+FBdv,http://purl.obolibrary.org/obo/FBdv_
+FBdv,http://purl.obolibrary.org/obo/FBdv_
+ZFA,http://purl.obolibrary.org/obo/ZFA_
+ZFA,http://purl.obolibrary.org/obo/ZFA_
+FIDEO,http://purl.obolibrary.org/obo/FIDEO_
+FIDEO,http://purl.obolibrary.org/obo/FIDEO_
+WBPhenotype,http://purl.obolibrary.org/obo/WBPhenotype_
+WBPhenotype,http://purl.obolibrary.org/obo/WBPhenotype_
+XAO,http://purl.obolibrary.org/obo/XAO_
+XAO,http://purl.obolibrary.org/obo/XAO_
+XCO,http://purl.obolibrary.org/obo/XCO_
+XCO,http://purl.obolibrary.org/obo/XCO_
+XLMOD,http://purl.obolibrary.org/obo/XLMOD_
+XLMOD,http://purl.obolibrary.org/obo/XLMOD_
+MAMO,http://purl.obolibrary.org/obo/MAMO_
+MAMO,http://purl.obolibrary.org/obo/MAMO_
+HANCESTRO,http://purl.obolibrary.org/obo/HANCESTRO_
+HANCESTRO,http://purl.obolibrary.org/obo/HANCESTRO_
+REX,http://purl.obolibrary.org/obo/REX_
+REX,http://purl.obolibrary.org/obo/REX_
+HAO,http://purl.obolibrary.org/obo/HAO_
+HAO,http://purl.obolibrary.org/obo/HAO_
+SIBO,http://purl.obolibrary.org/obo/SIBO_
+SIBO,http://purl.obolibrary.org/obo/SIBO_
+HOM,http://purl.obolibrary.org/obo/HOM_
+HOM,http://purl.obolibrary.org/obo/HOM_
+VariO,http://purl.obolibrary.org/obo/VariO_
+VariO,http://purl.obolibrary.org/obo/VariO_
+HsapDv,http://purl.obolibrary.org/obo/HsapDv_
+HsapDv,http://purl.obolibrary.org/obo/HsapDv_
+KISAO,http://purl.obolibrary.org/obo/KISAO_
+KISAO,http://purl.obolibrary.org/obo/KISAO_
+SBO,http://purl.obolibrary.org/obo/SBO_
+SBO,http://purl.obolibrary.org/obo/SBO_
+GEO,http://purl.obolibrary.org/obo/GEO_
+GEO,http://purl.obolibrary.org/obo/GEO_
+SCDO,http://purl.obolibrary.org/obo/SCDO_
+SCDO,http://purl.obolibrary.org/obo/SCDO_
+GNO,http://purl.obolibrary.org/obo/GNO_
+GNO,http://purl.obolibrary.org/obo/GNO_
+FIX,http://purl.obolibrary.org/obo/FIX_
+FIX,http://purl.obolibrary.org/obo/FIX_
+GO,http://purl.obolibrary.org/obo/GO_
+GO,http://purl.obolibrary.org/obo/GO_
+UBERON,http://purl.obolibrary.org/obo/UBERON_
+UBERON,http://purl.obolibrary.org/obo/UBERON_
+FYPO,http://purl.obolibrary.org/obo/FYPO_
+FYPO,http://purl.obolibrary.org/obo/FYPO_
+GSSO,http://purl.obolibrary.org/obo/GSSO_
+GSSO,http://purl.obolibrary.org/obo/GSSO_
+GECKO,http://purl.obolibrary.org/obo/GECKO_
+GECKO,http://purl.obolibrary.org/obo/GECKO_
+HP,http://purl.obolibrary.org/obo/HP_
+HP,http://purl.obolibrary.org/obo/HP_
+GENEPIO,http://purl.obolibrary.org/obo/GENEPIO_
+GENEPIO,http://purl.obolibrary.org/obo/GENEPIO_
+GENO,http://purl.obolibrary.org/obo/GENO_
+GENO,http://purl.obolibrary.org/obo/GENO_
+EHDAA2,http://purl.obolibrary.org/obo/EHDAA2_
+EHDAA2,http://purl.obolibrary.org/obo/EHDAA2_
+RNAO,http://purl.obolibrary.org/obo/RNAO_
+RNAO,http://purl.obolibrary.org/obo/RNAO_
+LABO,http://purl.obolibrary.org/obo/LABO_
+LABO,http://purl.obolibrary.org/obo/LABO_
+TADS,http://purl.obolibrary.org/obo/TADS_
+TADS,http://purl.obolibrary.org/obo/TADS_
+LEPAO,http://purl.obolibrary.org/obo/LEPAO_
+LEPAO,http://purl.obolibrary.org/obo/LEPAO_
+TGMA,http://purl.obolibrary.org/obo/TGMA_
+TGMA,http://purl.obolibrary.org/obo/TGMA_
+MA,http://purl.obolibrary.org/obo/MA_
+MA,http://purl.obolibrary.org/obo/MA_
+UPA,http://purl.obolibrary.org/obo/UPA_
+UPA,http://purl.obolibrary.org/obo/UPA_
+MAXO,http://purl.obolibrary.org/obo/MAXO_
+MAXO,http://purl.obolibrary.org/obo/MAXO_
+FMA,http://purl.obolibrary.org/obo/FMA_
+FMA,http://purl.obolibrary.org/obo/FMA_
+ICEO,http://purl.obolibrary.org/obo/ICEO_
+ICEO,http://purl.obolibrary.org/obo/ICEO_
+GAZ,http://purl.obolibrary.org/obo/GAZ_
+GAZ,http://purl.obolibrary.org/obo/GAZ_
+ICO,http://purl.obolibrary.org/obo/ICO_
+ICO,http://purl.obolibrary.org/obo/ICO_
+IDOMAL,http://purl.obolibrary.org/obo/IDOMAL_
+IDOMAL,http://purl.obolibrary.org/obo/IDOMAL_
+IDO,http://purl.obolibrary.org/obo/IDO_
+IDO,http://purl.obolibrary.org/obo/IDO_
+MIRO,http://purl.obolibrary.org/obo/MIRO_
+MIRO,http://purl.obolibrary.org/obo/MIRO_
+INO,http://purl.obolibrary.org/obo/INO_
+INO,http://purl.obolibrary.org/obo/INO_
+AEO,http://purl.obolibrary.org/obo/AEO_
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+APOLLO_SV,http://purl.obolibrary.org/obo/APOLLO_SV_
+TAHH,http://purl.obolibrary.org/obo/TAHH_
 TAHH,http://purl.obolibrary.org/obo/TAHH_
 PATO,http://purl.obolibrary.org/obo/PATO_
+PATO,http://purl.obolibrary.org/obo/PATO_
+ARO,http://purl.obolibrary.org/obo/ARO_
 ARO,http://purl.obolibrary.org/obo/ARO_
 TAO,http://purl.obolibrary.org/obo/TAO_
+TAO,http://purl.obolibrary.org/obo/TAO_
+PCL,http://purl.obolibrary.org/obo/PCL_
 PCL,http://purl.obolibrary.org/obo/PCL_
 BCO,http://purl.obolibrary.org/obo/BCO_
+BCO,http://purl.obolibrary.org/obo/BCO_
+VHOG,http://purl.obolibrary.org/obo/VHOG_
 VHOG,http://purl.obolibrary.org/obo/VHOG_
 PCO,http://purl.obolibrary.org/obo/PCO_
+PCO,http://purl.obolibrary.org/obo/PCO_
+BFO,http://purl.obolibrary.org/obo/BFO_
 BFO,http://purl.obolibrary.org/obo/BFO_
 PHIPO,http://purl.obolibrary.org/obo/PHIPO_
+PHIPO,http://purl.obolibrary.org/obo/PHIPO_
+CDAO,http://purl.obolibrary.org/obo/CDAO_
 CDAO,http://purl.obolibrary.org/obo/CDAO_
 PLANA,http://purl.obolibrary.org/obo/PLANA_
+PLANA,http://purl.obolibrary.org/obo/PLANA_
+CDNO,http://purl.obolibrary.org/obo/CDNO_
 CDNO,http://purl.obolibrary.org/obo/CDNO_
 PLANP,http://purl.obolibrary.org/obo/PLANP_
+PLANP,http://purl.obolibrary.org/obo/PLANP_
+CHEBI,http://purl.obolibrary.org/obo/CHEBI_
 CHEBI,http://purl.obolibrary.org/obo/CHEBI_
 PO,http://purl.obolibrary.org/obo/PO_
+PO,http://purl.obolibrary.org/obo/PO_
+CHEMINF,http://purl.obolibrary.org/obo/CHEMINF_
 CHEMINF,http://purl.obolibrary.org/obo/CHEMINF_
 PdumDv,http://purl.obolibrary.org/obo/PdumDv_
+PdumDv,http://purl.obolibrary.org/obo/PdumDv_
+PECO,http://purl.obolibrary.org/obo/PECO_
 PECO,http://purl.obolibrary.org/obo/PECO_
 CARO,http://purl.obolibrary.org/obo/CARO_
+CARO,http://purl.obolibrary.org/obo/CARO_
+CL,http://purl.obolibrary.org/obo/CL_
 CL,http://purl.obolibrary.org/obo/CL_
 PORO,http://purl.obolibrary.org/obo/PORO_
+PORO,http://purl.obolibrary.org/obo/PORO_
+CHIRO,http://purl.obolibrary.org/obo/CHIRO_
 CHIRO,http://purl.obolibrary.org/obo/CHIRO_
 PPO,http://purl.obolibrary.org/obo/PPO_
+PPO,http://purl.obolibrary.org/obo/PPO_
+CHMO,http://purl.obolibrary.org/obo/CHMO_
 CHMO,http://purl.obolibrary.org/obo/CHMO_
 PR,http://purl.obolibrary.org/obo/PR_
+PR,http://purl.obolibrary.org/obo/PR_
+CIDO,http://purl.obolibrary.org/obo/CIDO_
 CIDO,http://purl.obolibrary.org/obo/CIDO_
 PROCO,http://purl.obolibrary.org/obo/PROCO_
+PROCO,http://purl.obolibrary.org/obo/PROCO_
+CIO,http://purl.obolibrary.org/obo/CIO_
 CIO,http://purl.obolibrary.org/obo/CIO_
diff --git a/src/semsql/builder/prefixes/obo_prefixes.db b/src/semsql/builder/prefixes/obo_prefixes.db
index 38c84d89639eb56cb568c5e1e7d036af6eb27612..814f77040880e6dcc6bf4bca4c6389879d62a9dd 100644
GIT binary patch
diff --git a/src/semsql/builder/prefixes/prefixes.csv b/src/semsql/builder/prefixes/prefixes.csv
index 3c8ff58..88de6c2 100644
--- a/src/semsql/builder/prefixes/prefixes.csv
+++ b/src/semsql/builder/prefixes/prefixes.csv
@@ -65,257 +65,1024 @@ hgnc.genegroup,http://purl.obolibrary.org/obo/dictybase_
 EC,http://purl.obolibrary.org/obo/eccode_
 uniprot.obo,http://purl.obolibrary.org/obo/uniprot_
 uniprot.obo,http://purl.obolibrary.org/obo/uniprot_
+rhea,http://purl.obolibrary.org/obo/rhea_
+uniprot.obo,http://purl.obolibrary.org/obo/uniprot_
+drugbank,http://purl.obolibrary.org/obo/drugbank_
+drugbank,http://purl.obolibrary.org/obo/drugcentral_
+complexportal,http://purl.obolibrary.org/obo/complexportal_
+RBO,http://purl.obolibrary.org/obo/RBO_
+RBO,http://purl.obolibrary.org/obo/RBO_
+CLYH,http://purl.obolibrary.org/obo/CLYH_
+CLYH,http://purl.obolibrary.org/obo/CLYH_
+RO,http://purl.obolibrary.org/obo/RO_
+RO,http://purl.obolibrary.org/obo/RO_
+CMO,http://purl.obolibrary.org/obo/CMO_
+CMO,http://purl.obolibrary.org/obo/CMO_
+RS,http://purl.obolibrary.org/obo/RS_
+RS,http://purl.obolibrary.org/obo/RS_
+COB,http://purl.obolibrary.org/obo/COB_
+COB,http://purl.obolibrary.org/obo/COB_
+RXNO,http://purl.obolibrary.org/obo/RXNO_
+RXNO,http://purl.obolibrary.org/obo/RXNO_
+COLAO,http://purl.obolibrary.org/obo/COLAO_
+COLAO,http://purl.obolibrary.org/obo/COLAO_
+PSDO,http://purl.obolibrary.org/obo/PSDO_
+PSDO,http://purl.obolibrary.org/obo/PSDO_
+PSO,http://purl.obolibrary.org/obo/PSO_
+PSO,http://purl.obolibrary.org/obo/PSO_
+CLAO,http://purl.obolibrary.org/obo/CLAO_
+CLAO,http://purl.obolibrary.org/obo/CLAO_
+PW,http://purl.obolibrary.org/obo/PW_
+PW,http://purl.obolibrary.org/obo/PW_
+CLO,http://purl.obolibrary.org/obo/CLO_
+CLO,http://purl.obolibrary.org/obo/CLO_
+SEPIO,http://purl.obolibrary.org/obo/SEPIO_
+SEPIO,http://purl.obolibrary.org/obo/SEPIO_
+CRO,http://purl.obolibrary.org/obo/CRO_
+CRO,http://purl.obolibrary.org/obo/CRO_
+SO,http://purl.obolibrary.org/obo/SO_
+SO,http://purl.obolibrary.org/obo/SO_
+CTENO,http://purl.obolibrary.org/obo/CTENO_
+CTENO,http://purl.obolibrary.org/obo/CTENO_
+SPD,http://purl.obolibrary.org/obo/SPD_
+SPD,http://purl.obolibrary.org/obo/SPD_
+CTO,http://purl.obolibrary.org/obo/CTO_
+CTO,http://purl.obolibrary.org/obo/CTO_
+CVDO,http://purl.obolibrary.org/obo/CVDO_
+CVDO,http://purl.obolibrary.org/obo/CVDO_
+DISDRIV,http://purl.obolibrary.org/obo/DISDRIV_
+DISDRIV,http://purl.obolibrary.org/obo/DISDRIV_
+DOID,http://purl.obolibrary.org/obo/DOID_
+DOID,http://purl.obolibrary.org/obo/DOID_
+FBcv,http://purl.obolibrary.org/obo/FBcv_
+FBcv,http://purl.obolibrary.org/obo/FBcv_
+DRON,http://purl.obolibrary.org/obo/DRON_
+DRON,http://purl.obolibrary.org/obo/DRON_
+DDANAT,http://purl.obolibrary.org/obo/DDANAT_
+DDANAT,http://purl.obolibrary.org/obo/DDANAT_
+DDPHENO,http://purl.obolibrary.org/obo/DDPHENO_
+DDPHENO,http://purl.obolibrary.org/obo/DDPHENO_
+DIDEO,http://purl.obolibrary.org/obo/DIDEO_
+DIDEO,http://purl.obolibrary.org/obo/DIDEO_
+DUO,http://purl.obolibrary.org/obo/DUO_
+DUO,http://purl.obolibrary.org/obo/DUO_
+ECAO,http://purl.obolibrary.org/obo/ECAO_
+ECAO,http://purl.obolibrary.org/obo/ECAO_
+ECOCORE,http://purl.obolibrary.org/obo/ECOCORE_
+ECOCORE,http://purl.obolibrary.org/obo/ECOCORE_
+EUPATH,http://purl.obolibrary.org/obo/EUPATH_
+EUPATH,http://purl.obolibrary.org/obo/EUPATH_
+ExO,http://purl.obolibrary.org/obo/ExO_
+ExO,http://purl.obolibrary.org/obo/ExO_
+FAO,http://purl.obolibrary.org/obo/FAO_
+FAO,http://purl.obolibrary.org/obo/FAO_
+FBbi,http://purl.obolibrary.org/obo/FBbi_
+FBbi,http://purl.obolibrary.org/obo/FBbi_
+ECTO,http://purl.obolibrary.org/obo/ECTO_
+ECTO,http://purl.obolibrary.org/obo/ECTO_
+EMAPA,http://purl.obolibrary.org/obo/EMAPA_
+EMAPA,http://purl.obolibrary.org/obo/EMAPA_
+ENVO,http://purl.obolibrary.org/obo/ENVO_
+ENVO,http://purl.obolibrary.org/obo/ENVO_
+EPIO,http://purl.obolibrary.org/obo/EPIO_
+EPIO,http://purl.obolibrary.org/obo/EPIO_
+FBbt,http://purl.obolibrary.org/obo/FBbt_
+FBbt,http://purl.obolibrary.org/obo/FBbt_
+FBcv,http://purl.obolibrary.org/obo/FBcv_
+FBcv,http://purl.obolibrary.org/obo/FBcv_
+VSAO,http://purl.obolibrary.org/obo/VSAO_
+VSAO,http://purl.obolibrary.org/obo/VSAO_
+YPO,http://purl.obolibrary.org/obo/YPO_
+YPO,http://purl.obolibrary.org/obo/YPO_
+ZEA,http://purl.obolibrary.org/obo/ZEA_
+ZEA,http://purl.obolibrary.org/obo/ZEA_
+SWO,http://purl.obolibrary.org/obo/SWO_
+SWO,http://purl.obolibrary.org/obo/SWO_
+SYMP,http://purl.obolibrary.org/obo/SYMP_
+SYMP,http://purl.obolibrary.org/obo/SYMP_
+TAXRANK,http://purl.obolibrary.org/obo/TAXRANK_
+TAXRANK,http://purl.obolibrary.org/obo/TAXRANK_
+TO,http://purl.obolibrary.org/obo/TO_
+TO,http://purl.obolibrary.org/obo/TO_
+STATO,http://purl.obolibrary.org/obo/STATO_
+STATO,http://purl.obolibrary.org/obo/STATO_
+VT,http://purl.obolibrary.org/obo/VT_
+VT,http://purl.obolibrary.org/obo/VT_
+VTO,http://purl.obolibrary.org/obo/VTO_
+VTO,http://purl.obolibrary.org/obo/VTO_
+WBbt,http://purl.obolibrary.org/obo/WBbt_
+WBbt,http://purl.obolibrary.org/obo/WBbt_
+WBls,http://purl.obolibrary.org/obo/WBls_
+WBls,http://purl.obolibrary.org/obo/WBls_
+VBO,http://purl.obolibrary.org/obo/VBO_
+VBO,http://purl.obolibrary.org/obo/VBO_
+VO,http://purl.obolibrary.org/obo/VO_
+VO,http://purl.obolibrary.org/obo/VO_
+UPHENO,http://purl.obolibrary.org/obo/UPHENO_
+UPHENO,http://purl.obolibrary.org/obo/UPHENO_
+TRANS,http://purl.obolibrary.org/obo/TRANS_
+TRANS,http://purl.obolibrary.org/obo/TRANS_
+TTO,http://purl.obolibrary.org/obo/TTO_
+TTO,http://purl.obolibrary.org/obo/TTO_
+TXPO,http://purl.obolibrary.org/obo/TXPO_
+TXPO,http://purl.obolibrary.org/obo/TXPO_
+UO,http://purl.obolibrary.org/obo/UO_
+UO,http://purl.obolibrary.org/obo/UO_
+ZFS,http://purl.obolibrary.org/obo/ZFS_
+ZFS,http://purl.obolibrary.org/obo/ZFS_
+FLOPO,http://purl.obolibrary.org/obo/FLOPO_
+FLOPO,http://purl.obolibrary.org/obo/FLOPO_
+ZP,http://purl.obolibrary.org/obo/ZP_
+ZP,http://purl.obolibrary.org/obo/ZP_
+FOBI,http://purl.obolibrary.org/obo/FOBI_
+FOBI,http://purl.obolibrary.org/obo/FOBI_
+ECO,http://purl.obolibrary.org/obo/ECO_
+ECO,http://purl.obolibrary.org/obo/ECO_
+FOODON,http://purl.obolibrary.org/obo/FOODON_
+FOODON,http://purl.obolibrary.org/obo/FOODON_
+NOMEN,http://purl.obolibrary.org/obo/NOMEN_
+NOMEN,http://purl.obolibrary.org/obo/NOMEN_
+FOVT,http://purl.obolibrary.org/obo/FOVT_
+FOVT,http://purl.obolibrary.org/obo/FOVT_
+XPO,http://purl.obolibrary.org/obo/XPO_
+XPO,http://purl.obolibrary.org/obo/XPO_
+ZECO,http://purl.obolibrary.org/obo/ZECO_
+ZECO,http://purl.obolibrary.org/obo/ZECO_
+FBdv,http://purl.obolibrary.org/obo/FBdv_
+FBdv,http://purl.obolibrary.org/obo/FBdv_
+ZFA,http://purl.obolibrary.org/obo/ZFA_
+ZFA,http://purl.obolibrary.org/obo/ZFA_
+FIDEO,http://purl.obolibrary.org/obo/FIDEO_
+FIDEO,http://purl.obolibrary.org/obo/FIDEO_
+WBPhenotype,http://purl.obolibrary.org/obo/WBPhenotype_
+WBPhenotype,http://purl.obolibrary.org/obo/WBPhenotype_
+XAO,http://purl.obolibrary.org/obo/XAO_
+XAO,http://purl.obolibrary.org/obo/XAO_
+XCO,http://purl.obolibrary.org/obo/XCO_
+XCO,http://purl.obolibrary.org/obo/XCO_
+XLMOD,http://purl.obolibrary.org/obo/XLMOD_
+XLMOD,http://purl.obolibrary.org/obo/XLMOD_
+MAMO,http://purl.obolibrary.org/obo/MAMO_
+MAMO,http://purl.obolibrary.org/obo/MAMO_
+HANCESTRO,http://purl.obolibrary.org/obo/HANCESTRO_
+HANCESTRO,http://purl.obolibrary.org/obo/HANCESTRO_
+REX,http://purl.obolibrary.org/obo/REX_
+REX,http://purl.obolibrary.org/obo/REX_
+HAO,http://purl.obolibrary.org/obo/HAO_
+HAO,http://purl.obolibrary.org/obo/HAO_
+SIBO,http://purl.obolibrary.org/obo/SIBO_
+SIBO,http://purl.obolibrary.org/obo/SIBO_
+HOM,http://purl.obolibrary.org/obo/HOM_
+HOM,http://purl.obolibrary.org/obo/HOM_
+VariO,http://purl.obolibrary.org/obo/VariO_
+VariO,http://purl.obolibrary.org/obo/VariO_
+HsapDv,http://purl.obolibrary.org/obo/HsapDv_
+HsapDv,http://purl.obolibrary.org/obo/HsapDv_
+KISAO,http://purl.obolibrary.org/obo/KISAO_
+KISAO,http://purl.obolibrary.org/obo/KISAO_
+SBO,http://purl.obolibrary.org/obo/SBO_
+SBO,http://purl.obolibrary.org/obo/SBO_
+GEO,http://purl.obolibrary.org/obo/GEO_
+GEO,http://purl.obolibrary.org/obo/GEO_
+SCDO,http://purl.obolibrary.org/obo/SCDO_
+SCDO,http://purl.obolibrary.org/obo/SCDO_
+GNO,http://purl.obolibrary.org/obo/GNO_
+GNO,http://purl.obolibrary.org/obo/GNO_
+FIX,http://purl.obolibrary.org/obo/FIX_
+FIX,http://purl.obolibrary.org/obo/FIX_
+GO,http://purl.obolibrary.org/obo/GO_
+GO,http://purl.obolibrary.org/obo/GO_
+UBERON,http://purl.obolibrary.org/obo/UBERON_
+UBERON,http://purl.obolibrary.org/obo/UBERON_
+FYPO,http://purl.obolibrary.org/obo/FYPO_
+FYPO,http://purl.obolibrary.org/obo/FYPO_
+GSSO,http://purl.obolibrary.org/obo/GSSO_
+GSSO,http://purl.obolibrary.org/obo/GSSO_
+GECKO,http://purl.obolibrary.org/obo/GECKO_
+GECKO,http://purl.obolibrary.org/obo/GECKO_
+HP,http://purl.obolibrary.org/obo/HP_
+HP,http://purl.obolibrary.org/obo/HP_
+GENEPIO,http://purl.obolibrary.org/obo/GENEPIO_
+GENEPIO,http://purl.obolibrary.org/obo/GENEPIO_
+GENO,http://purl.obolibrary.org/obo/GENO_
+GENO,http://purl.obolibrary.org/obo/GENO_
+EHDAA2,http://purl.obolibrary.org/obo/EHDAA2_
+EHDAA2,http://purl.obolibrary.org/obo/EHDAA2_
+RNAO,http://purl.obolibrary.org/obo/RNAO_
+RNAO,http://purl.obolibrary.org/obo/RNAO_
+LABO,http://purl.obolibrary.org/obo/LABO_
+LABO,http://purl.obolibrary.org/obo/LABO_
+TADS,http://purl.obolibrary.org/obo/TADS_
+TADS,http://purl.obolibrary.org/obo/TADS_
+LEPAO,http://purl.obolibrary.org/obo/LEPAO_
+LEPAO,http://purl.obolibrary.org/obo/LEPAO_
+TGMA,http://purl.obolibrary.org/obo/TGMA_
+TGMA,http://purl.obolibrary.org/obo/TGMA_
+MA,http://purl.obolibrary.org/obo/MA_
+MA,http://purl.obolibrary.org/obo/MA_
+UPA,http://purl.obolibrary.org/obo/UPA_
+UPA,http://purl.obolibrary.org/obo/UPA_
+MAXO,http://purl.obolibrary.org/obo/MAXO_
+MAXO,http://purl.obolibrary.org/obo/MAXO_
+FMA,http://purl.obolibrary.org/obo/FMA_
+FMA,http://purl.obolibrary.org/obo/FMA_
+ICEO,http://purl.obolibrary.org/obo/ICEO_
+ICEO,http://purl.obolibrary.org/obo/ICEO_
+GAZ,http://purl.obolibrary.org/obo/GAZ_
+GAZ,http://purl.obolibrary.org/obo/GAZ_
+ICO,http://purl.obolibrary.org/obo/ICO_
+ICO,http://purl.obolibrary.org/obo/ICO_
+IDOMAL,http://purl.obolibrary.org/obo/IDOMAL_
+IDOMAL,http://purl.obolibrary.org/obo/IDOMAL_
+IDO,http://purl.obolibrary.org/obo/IDO_
+IDO,http://purl.obolibrary.org/obo/IDO_
+MIRO,http://purl.obolibrary.org/obo/MIRO_
+MIRO,http://purl.obolibrary.org/obo/MIRO_
+INO,http://purl.obolibrary.org/obo/INO_
+INO,http://purl.obolibrary.org/obo/INO_
+AEO,http://purl.obolibrary.org/obo/AEO_
+AEO,http://purl.obolibrary.org/obo/AEO_
+HSO,http://purl.obolibrary.org/obo/HSO_
+HSO,http://purl.obolibrary.org/obo/HSO_
+CEPH,http://purl.obolibrary.org/obo/CEPH_
+CEPH,http://purl.obolibrary.org/obo/CEPH_
+HTN,http://purl.obolibrary.org/obo/HTN_
+HTN,http://purl.obolibrary.org/obo/HTN_
+IAO,http://purl.obolibrary.org/obo/IAO_
+IAO,http://purl.obolibrary.org/obo/IAO_
+ADW,http://purl.obolibrary.org/obo/ADW_
+ADW,http://purl.obolibrary.org/obo/ADW_
+AERO,http://purl.obolibrary.org/obo/AERO_
+AERO,http://purl.obolibrary.org/obo/AERO_
+MFMO,http://purl.obolibrary.org/obo/MFMO_
+MFMO,http://purl.obolibrary.org/obo/MFMO_
+CMF,http://purl.obolibrary.org/obo/CMF_
+CMF,http://purl.obolibrary.org/obo/CMF_
+MICRO,http://purl.obolibrary.org/obo/MICRO_
+MICRO,http://purl.obolibrary.org/obo/MICRO_
+DC_CL,http://purl.obolibrary.org/obo/DC_CL_
+DC_CL,http://purl.obolibrary.org/obo/DC_CL_
+MMO,http://purl.obolibrary.org/obo/MMO_
+MMO,http://purl.obolibrary.org/obo/MMO_
+DINTO,http://purl.obolibrary.org/obo/DINTO_
+DINTO,http://purl.obolibrary.org/obo/DINTO_
+MmusDv,http://purl.obolibrary.org/obo/MmusDv_
+MmusDv,http://purl.obolibrary.org/obo/MmusDv_
+EHDA,http://purl.obolibrary.org/obo/EHDA_
+EHDA,http://purl.obolibrary.org/obo/EHDA_
+MOD,http://purl.obolibrary.org/obo/MOD_
+MOD,http://purl.obolibrary.org/obo/MOD_
+ATO,http://purl.obolibrary.org/obo/ATO_
+ATO,http://purl.obolibrary.org/obo/ATO_
+MFOEM,http://purl.obolibrary.org/obo/MFOEM_
+MFOEM,http://purl.obolibrary.org/obo/MFOEM_
+BCGO,http://purl.obolibrary.org/obo/BCGO_
+BCGO,http://purl.obolibrary.org/obo/BCGO_
+MFOMD,http://purl.obolibrary.org/obo/MFOMD_
+MFOMD,http://purl.obolibrary.org/obo/MFOMD_
+BILA,http://purl.obolibrary.org/obo/BILA_
+BILA,http://purl.obolibrary.org/obo/BILA_
+MI,http://purl.obolibrary.org/obo/MI_
+MI,http://purl.obolibrary.org/obo/MI_
+BOOTSTREP,http://purl.obolibrary.org/obo/BOOTSTREP_
+BOOTSTREP,http://purl.obolibrary.org/obo/BOOTSTREP_
+MIAPA,http://purl.obolibrary.org/obo/MIAPA_
+MIAPA,http://purl.obolibrary.org/obo/MIAPA_
+AAO,http://purl.obolibrary.org/obo/AAO_
+AAO,http://purl.obolibrary.org/obo/AAO_
+MCO,http://purl.obolibrary.org/obo/MCO_
+MCO,http://purl.obolibrary.org/obo/MCO_
+MF,http://purl.obolibrary.org/obo/MF_
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 CIDO,http://purl.obolibrary.org/obo/CIDO_
 PROCO,http://purl.obolibrary.org/obo/PROCO_
+PROCO,http://purl.obolibrary.org/obo/PROCO_
+CIO,http://purl.obolibrary.org/obo/CIO_
 CIO,http://purl.obolibrary.org/obo/CIO_
diff --git a/src/semsql/builder/prefixes/prefixes_local.csv b/src/semsql/builder/prefixes/prefixes_local.csv
index df21910..8038244 100644
--- a/src/semsql/builder/prefixes/prefixes_local.csv
+++ b/src/semsql/builder/prefixes/prefixes_local.csv
@@ -13,3 +13,8 @@ hgnc.genegroup,http://purl.obolibrary.org/obo/dictybase_
 EC,http://purl.obolibrary.org/obo/eccode_
 uniprot.obo,http://purl.obolibrary.org/obo/uniprot_
 uniprot.obo,http://purl.obolibrary.org/obo/uniprot_
+rhea,http://purl.obolibrary.org/obo/rhea_
+uniprot.obo,http://purl.obolibrary.org/obo/uniprot_
+drugbank,http://purl.obolibrary.org/obo/drugbank_
+drugbank,http://purl.obolibrary.org/obo/drugcentral_
+complexportal,http://purl.obolibrary.org/obo/complexportal_
diff --git a/src/semsql/builder/registry/ontologies.yaml b/src/semsql/builder/registry/ontologies.yaml
index 5f98321..c4dde36 100644
--- a/src/semsql/builder/registry/ontologies.yaml
+++ b/src/semsql/builder/registry/ontologies.yaml
@@ -143,3 +143,24 @@ ontologies:
     compression: gzip
     prefixmap:
       uniprot.obo: http://purl.obolibrary.org/obo/uniprot_
+  rhea:
+    url: https://github.com/biopragmatics/obo-db-ingest/raw/main/export/rhea/122/rhea.owl.gz
+    compression: gzip
+    prefixmap:
+      rhea: http://purl.obolibrary.org/obo/rhea_
+      uniprot.obo: http://purl.obolibrary.org/obo/uniprot_
+  drugbank:
+    url: https://github.com/biopragmatics/obo-db-ingest/raw/main/export/drugbank/5.1.9/drugbank.owl.gz
+    compression: gzip
+    prefixmap:
+      drugbank: http://purl.obolibrary.org/obo/drugbank_
+  drugcentral:
+    url: https://github.com/biopragmatics/obo-db-ingest/raw/main/export/drugcentral.owl.gz
+    compression: gzip
+    prefixmap:
+      drugbank: http://purl.obolibrary.org/obo/drugcentral_
+  complexportal:
+    url: https://github.com/biopragmatics/obo-db-ingest/raw/main/export/complexportal/2022-02-03/complexportal.owl.gz
+    compression: gzip
+    prefixmap:
+      complexportal: http://purl.obolibrary.org/obo/complexportal_
diff --git a/src/semsql/builder/sql_schema/rdf.sql b/src/semsql/builder/sql_schema/rdf.sql
index 19af11f..263cb94 100644
--- a/src/semsql/builder/sql_schema/rdf.sql
+++ b/src/semsql/builder/sql_schema/rdf.sql
@@ -123,6 +123,10 @@
 --     * Slot: language Description: the human language in which the value is encoded, e.g. en
 -- # Class: "node" Description: "The basic unit of representation in an RDF or OWL graph"
 --     * Slot: id Description: An identifier for an element. Note blank node ids are not unique across databases
+-- # Class: "node_identifier" Description: ""
+--     * Slot: id Description: An identifier for an element. Note blank node ids are not unique across databases
+--     * Slot: prefix Description: A standardized prefix such as 'GO' or 'rdf' or 'FlyBase'
+--     * Slot: local_identifier Description: The part of a CURIE after the colon
 -- # Class: "blank_node" Description: "A node with an ID that is not preserved between databases"
 --     * Slot: id Description: An identifier for an element. Note blank node ids are not unique across databases
 -- # Class: "rdf_list_node" Description: "A node representing an RDF list. Note that you will not likely need to use this directly."
@@ -296,6 +300,12 @@ CREATE TABLE node (
 	id TEXT, 
 	PRIMARY KEY (id)
 );
+CREATE TABLE node_identifier (
+	id TEXT, 
+	prefix TEXT, 
+	local_identifier TEXT, 
+	PRIMARY KEY (id)
+);
 CREATE TABLE blank_node (
 	id TEXT, 
 	PRIMARY KEY (id)
@@ -398,6 +408,13 @@ CREATE VIEW rdf_list_member_statement AS SELECT
 DROP TABLE node;
 CREATE VIEW node AS SELECT distinct(subject) AS id FROM statements UNION SELECT distinct(object) AS id FROM statements WHERE datatype IS NOT NULL;
 
+DROP TABLE node_identifier;
+CREATE VIEW node_identifier AS SELECT
+    id AS id,
+    substr(id,0, instr(id,':')) AS prefix,
+    substr(id,instr(id,':')+1) AS local_identifier
+  FROM node;
+
 DROP TABLE blank_node;
 CREATE VIEW blank_node AS SELECT * FROM node WHERE id LIKE '_:%';
 
diff --git a/src/semsql/builder/sql_schema/semsql.sql b/src/semsql/builder/sql_schema/semsql.sql
index cb1d788..aaf8d4d 100644
--- a/src/semsql/builder/sql_schema/semsql.sql
+++ b/src/semsql/builder/sql_schema/semsql.sql
@@ -416,6 +416,10 @@
 --     * Slot: language Description: the human language in which the value is encoded, e.g. en
 -- # Class: "node" Description: "The basic unit of representation in an RDF or OWL graph"
 --     * Slot: id Description: An identifier for an element. Note blank node ids are not unique across databases
+-- # Class: "node_identifier" Description: ""
+--     * Slot: id Description: An identifier for an element. Note blank node ids are not unique across databases
+--     * Slot: prefix Description: A standardized prefix such as 'GO' or 'rdf' or 'FlyBase'
+--     * Slot: local_identifier Description: The part of a CURIE after the colon
 -- # Class: "blank_node" Description: "A node with an ID that is not preserved between databases"
 --     * Slot: id Description: An identifier for an element. Note blank node ids are not unique across databases
 -- # Class: "rdf_list_node" Description: "A node representing an RDF list. Note that you will not likely need to use this directly."
@@ -1060,6 +1064,12 @@ CREATE TABLE node (
 	id TEXT, 
 	PRIMARY KEY (id)
 );
+CREATE TABLE node_identifier (
+	id TEXT, 
+	prefix TEXT, 
+	local_identifier TEXT, 
+	PRIMARY KEY (id)
+);
 CREATE TABLE blank_node (
 	id TEXT, 
 	PRIMARY KEY (id)
@@ -1496,6 +1506,13 @@ CREATE VIEW rdf_list_member_statement AS SELECT
 DROP TABLE node;
 CREATE VIEW node AS SELECT distinct(subject) AS id FROM statements UNION SELECT distinct(object) AS id FROM statements WHERE datatype IS NOT NULL;
 
+DROP TABLE node_identifier;
+CREATE VIEW node_identifier AS SELECT
+    id AS id,
+    substr(id,0, instr(id,':')) AS prefix,
+    substr(id,instr(id,':')+1) AS local_identifier
+  FROM node;
+
 DROP TABLE blank_node;
 CREATE VIEW blank_node AS SELECT * FROM node WHERE id LIKE '_:%';
 
diff --git a/src/semsql/linkml/rdf.yaml b/src/semsql/linkml/rdf.yaml
index 2a964b8..8073cba 100644
--- a/src/semsql/linkml/rdf.yaml
+++ b/src/semsql/linkml/rdf.yaml
@@ -99,6 +99,14 @@ slots:
     description: The base URI a prefix will expand to
     slot_uri: sh:namespace
     range: uri
+  local_identifier:
+    description: The part of a CURIE after the colon
+    comments:
+      - for OBOs this is frequently a string of zero-padded digits, but this is not always the case
+    aliases:
+      - code
+      - accession
+    range: string
   description:
     slot_uri: dcterms:description
 classes:
@@ -257,6 +265,19 @@ classes:
       AS id FROM statements WHERE datatype IS NOT NULL
     slots:
     - id
+  node_identifier:
+    comments:
+      - |-
+        sqlview>>
+          SELECT
+            id AS id,
+            substr(id,0, instr(id,':')) AS prefix,
+            substr(id,instr(id,':')+1) AS local_identifier
+          FROM node
+    slots:
+      - id
+      - prefix
+      - local_identifier
   blank_node:
     description: A node with an ID that is not preserved between databases
     comments:
diff --git a/src/semsql/linkml/semsql.yaml b/src/semsql/linkml/semsql.yaml
index 616f7c9..6eafad8 100644
--- a/src/semsql/linkml/semsql.yaml
+++ b/src/semsql/linkml/semsql.yaml
@@ -47,4 +47,4 @@ imports:
   - obo
   - omo
   - relation_graph
-  - term_associations
\ No newline at end of file
+  - term_associations
diff --git a/src/semsql/sqla/omo.py b/src/semsql/sqla/omo.py
index 5373f13..c1b1eb8 100644
--- a/src/semsql/sqla/omo.py
+++ b/src/semsql/sqla/omo.py
@@ -68,6 +68,19 @@ def __repr__(self):
         return f"node(id={self.id},)"
 
 
+class NodeIdentifier(Base):
+    """ """
+
+    __tablename__ = "node_identifier"
+
+    id = Column(Text(), primary_key=True)
+    prefix = Column(Text(), primary_key=True)
+    local_identifier = Column(Text(), primary_key=True)
+
+    def __repr__(self):
+        return f"node_identifier(id={self.id},prefix={self.prefix},local_identifier={self.local_identifier},)"
+
+
 class RdfLevelSummaryStatistic(Base):
     """
     Abstract grouping for views/classes that provide some kind of count summary about an individual element
@@ -82,6 +95,21 @@ def __repr__(self):
         return f"rdf_level_summary_statistic(element={self.element},count_value={self.count_value},)"
 
 
+class Orcid(Node):
+    """ """
+
+    __tablename__ = "orcid"
+
+    label = Column(Text(), primary_key=True)
+    id = Column(Text(), primary_key=True)
+
+    def __repr__(self):
+        return f"orcid(label={self.label},id={self.id},)"
+
+    # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html
+    __mapper_args__ = {"concrete": True}
+
+
 class OntologyNode(Node):
     """
     A node representing an ontology
@@ -161,11 +189,13 @@ class OwlAxiomAnnotation(Statements):
 
     __tablename__ = "owl_axiom_annotation"
 
-    axiom_predicate = Column(Text(), primary_key=True)
-    axiom_object = Column(Text(), primary_key=True)
-    axiom_value = Column(Text(), primary_key=True)
-    axiom_language = Column(Text(), primary_key=True)
-    axiom_datatype = Column(Text(), primary_key=True)
+    annotation_subject = Column(Text(), primary_key=True)
+    annotation_predicate = Column(Text(), primary_key=True)
+    annotation_object = Column(Text(), primary_key=True)
+    annotation_value = Column(Text(), primary_key=True)
+    annotation_language = Column(Text(), primary_key=True)
+    annotation_datatype = Column(Text(), primary_key=True)
+    id = Column(Text(), primary_key=True)
     stanza = Column(Text(), primary_key=True)
     subject = Column(Text(), primary_key=True)
     predicate = Column(Text(), primary_key=True)
@@ -175,7 +205,7 @@ class OwlAxiomAnnotation(Statements):
     language = Column(Text(), primary_key=True)
 
     def __repr__(self):
-        return f"owl_axiom_annotation(axiom_predicate={self.axiom_predicate},axiom_object={self.axiom_object},axiom_value={self.axiom_value},axiom_language={self.axiom_language},axiom_datatype={self.axiom_datatype},stanza={self.stanza},subject={self.subject},predicate={self.predicate},object={self.object},value={self.value},datatype={self.datatype},language={self.language},)"
+        return f"owl_axiom_annotation(annotation_subject={self.annotation_subject},annotation_predicate={self.annotation_predicate},annotation_object={self.annotation_object},annotation_value={self.annotation_value},annotation_language={self.annotation_language},annotation_datatype={self.annotation_datatype},id={self.id},stanza={self.stanza},subject={self.subject},predicate={self.predicate},object={self.object},value={self.value},datatype={self.datatype},language={self.language},)"
 
     # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html
     __mapper_args__ = {"concrete": True}
@@ -512,16 +542,58 @@ def __repr__(self):
     __mapper_args__ = {"concrete": True}
 
 
+class Contributor(NodeToNodeStatement):
+    """ """
+
+    __tablename__ = "contributor"
+
+    stanza = Column(Text(), primary_key=True)
+    subject = Column(Text(), primary_key=True)
+    predicate = Column(Text(), primary_key=True)
+    object = Column(Text(), primary_key=True)
+    value = Column(Text(), primary_key=True)
+    datatype = Column(Text(), primary_key=True)
+    language = Column(Text(), primary_key=True)
+
+    def __repr__(self):
+        return f"contributor(stanza={self.stanza},subject={self.subject},predicate={self.predicate},object={self.object},value={self.value},datatype={self.datatype},language={self.language},)"
+
+    # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html
+    __mapper_args__ = {"concrete": True}
+
+
+class Creator(NodeToNodeStatement):
+    """ """
+
+    __tablename__ = "creator"
+
+    stanza = Column(Text(), primary_key=True)
+    subject = Column(Text(), primary_key=True)
+    predicate = Column(Text(), primary_key=True)
+    object = Column(Text(), primary_key=True)
+    value = Column(Text(), primary_key=True)
+    datatype = Column(Text(), primary_key=True)
+    language = Column(Text(), primary_key=True)
+
+    def __repr__(self):
+        return f"creator(stanza={self.stanza},subject={self.subject},predicate={self.predicate},object={self.object},value={self.value},datatype={self.datatype},language={self.language},)"
+
+    # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html
+    __mapper_args__ = {"concrete": True}
+
+
 class AxiomDbxrefAnnotation(OwlAxiomAnnotation):
     """ """
 
     __tablename__ = "axiom_dbxref_annotation"
 
-    axiom_predicate = Column(Text(), primary_key=True)
-    axiom_object = Column(Text(), primary_key=True)
-    axiom_value = Column(Text(), primary_key=True)
-    axiom_language = Column(Text(), primary_key=True)
-    axiom_datatype = Column(Text(), primary_key=True)
+    annotation_subject = Column(Text(), primary_key=True)
+    annotation_predicate = Column(Text(), primary_key=True)
+    annotation_object = Column(Text(), primary_key=True)
+    annotation_value = Column(Text(), primary_key=True)
+    annotation_language = Column(Text(), primary_key=True)
+    annotation_datatype = Column(Text(), primary_key=True)
+    id = Column(Text(), primary_key=True)
     stanza = Column(Text(), primary_key=True)
     subject = Column(Text(), primary_key=True)
     predicate = Column(Text(), primary_key=True)
@@ -531,7 +603,7 @@ class AxiomDbxrefAnnotation(OwlAxiomAnnotation):
     language = Column(Text(), primary_key=True)
 
     def __repr__(self):
-        return f"axiom_dbxref_annotation(axiom_predicate={self.axiom_predicate},axiom_object={self.axiom_object},axiom_value={self.axiom_value},axiom_language={self.axiom_language},axiom_datatype={self.axiom_datatype},stanza={self.stanza},subject={self.subject},predicate={self.predicate},object={self.object},value={self.value},datatype={self.datatype},language={self.language},)"
+        return f"axiom_dbxref_annotation(annotation_subject={self.annotation_subject},annotation_predicate={self.annotation_predicate},annotation_object={self.annotation_object},annotation_value={self.annotation_value},annotation_language={self.annotation_language},annotation_datatype={self.annotation_datatype},id={self.id},stanza={self.stanza},subject={self.subject},predicate={self.predicate},object={self.object},value={self.value},datatype={self.datatype},language={self.language},)"
 
     # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html
     __mapper_args__ = {"concrete": True}
diff --git a/src/semsql/sqla/owl.py b/src/semsql/sqla/owl.py
index ef4fce7..fff6927 100644
--- a/src/semsql/sqla/owl.py
+++ b/src/semsql/sqla/owl.py
@@ -68,6 +68,19 @@ def __repr__(self):
         return f"node(id={self.id},)"
 
 
+class NodeIdentifier(Base):
+    """ """
+
+    __tablename__ = "node_identifier"
+
+    id = Column(Text(), primary_key=True)
+    prefix = Column(Text(), primary_key=True)
+    local_identifier = Column(Text(), primary_key=True)
+
+    def __repr__(self):
+        return f"node_identifier(id={self.id},prefix={self.prefix},local_identifier={self.local_identifier},)"
+
+
 class RdfLevelSummaryStatistic(Base):
     """
     Abstract grouping for views/classes that provide some kind of count summary about an individual element
diff --git a/src/semsql/sqla/rdf.py b/src/semsql/sqla/rdf.py
index d0e8abe..2e9d0e8 100644
--- a/src/semsql/sqla/rdf.py
+++ b/src/semsql/sqla/rdf.py
@@ -53,6 +53,19 @@ def __repr__(self):
         return f"node(id={self.id},)"
 
 
+class NodeIdentifier(Base):
+    """ """
+
+    __tablename__ = "node_identifier"
+
+    id = Column(Text(), primary_key=True)
+    prefix = Column(Text(), primary_key=True)
+    local_identifier = Column(Text(), primary_key=True)
+
+    def __repr__(self):
+        return f"node_identifier(id={self.id},prefix={self.prefix},local_identifier={self.local_identifier},)"
+
+
 class RdfLevelSummaryStatistic(Base):
     """
     Abstract grouping for views/classes that provide some kind of count summary about an individual element
diff --git a/src/semsql/sqla/semsql.py b/src/semsql/sqla/semsql.py
index 07a4a06..589f0ec 100644
--- a/src/semsql/sqla/semsql.py
+++ b/src/semsql/sqla/semsql.py
@@ -87,6 +87,19 @@ def __repr__(self):
         return f"node(id={self.id},)"
 
 
+class NodeIdentifier(Base):
+    """ """
+
+    __tablename__ = "node_identifier"
+
+    id = Column(Text(), primary_key=True)
+    prefix = Column(Text(), primary_key=True)
+    local_identifier = Column(Text(), primary_key=True)
+
+    def __repr__(self):
+        return f"node_identifier(id={self.id},prefix={self.prefix},local_identifier={self.local_identifier},)"
+
+
 class RdfLevelSummaryStatistic(Base):
     """
     Abstract grouping for views/classes that provide some kind of count summary about an individual element
@@ -145,6 +158,21 @@ def __repr__(self):
         return f"problem(subject={self.subject},predicate={self.predicate},value={self.value},)"
 
 
+class Orcid(Node):
+    """ """
+
+    __tablename__ = "orcid"
+
+    label = Column(Text(), primary_key=True)
+    id = Column(Text(), primary_key=True)
+
+    def __repr__(self):
+        return f"orcid(label={self.label},id={self.id},)"
+
+    # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html
+    __mapper_args__ = {"concrete": True}
+
+
 class OntologyNode(Node):
     """
     A node representing an ontology
@@ -756,6 +784,46 @@ def __repr__(self):
     __mapper_args__ = {"concrete": True}
 
 
+class Contributor(NodeToNodeStatement):
+    """ """
+
+    __tablename__ = "contributor"
+
+    stanza = Column(Text(), primary_key=True)
+    subject = Column(Text(), primary_key=True)
+    predicate = Column(Text(), primary_key=True)
+    object = Column(Text(), primary_key=True)
+    value = Column(Text(), primary_key=True)
+    datatype = Column(Text(), primary_key=True)
+    language = Column(Text(), primary_key=True)
+
+    def __repr__(self):
+        return f"contributor(stanza={self.stanza},subject={self.subject},predicate={self.predicate},object={self.object},value={self.value},datatype={self.datatype},language={self.language},)"
+
+    # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html
+    __mapper_args__ = {"concrete": True}
+
+
+class Creator(NodeToNodeStatement):
+    """ """
+
+    __tablename__ = "creator"
+
+    stanza = Column(Text(), primary_key=True)
+    subject = Column(Text(), primary_key=True)
+    predicate = Column(Text(), primary_key=True)
+    object = Column(Text(), primary_key=True)
+    value = Column(Text(), primary_key=True)
+    datatype = Column(Text(), primary_key=True)
+    language = Column(Text(), primary_key=True)
+
+    def __repr__(self):
+        return f"creator(stanza={self.stanza},subject={self.subject},predicate={self.predicate},object={self.object},value={self.value},datatype={self.datatype},language={self.language},)"
+
+    # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html
+    __mapper_args__ = {"concrete": True}
+
+
 class AxiomDbxrefAnnotation(OwlAxiomAnnotation):
     """ """
 
diff --git a/tests/inputs/go-nucleus.db b/tests/inputs/go-nucleus.db
index f406bd1a3cbeb0c616ca8aea963f333b863ac031..836a24f8b26dc45fe567534c183379cca46f1665 100644
GIT binary patch
diff --git a/tests/test_orm/test_basic_sqla.py b/tests/test_orm/test_basic_sqla.py
index 10c038b..e305013 100644
--- a/tests/test_orm/test_basic_sqla.py
+++ b/tests/test_orm/test_basic_sqla.py
@@ -6,7 +6,7 @@
 from sqlalchemy.orm import aliased, sessionmaker
 
 from semsql.sqla.semsql import (OwlAxiomAnnotation, OwlSomeValuesFrom,
-                                RdfsLabelStatement, RdfsSubclassOfStatement)
+                                RdfsLabelStatement, RdfsSubclassOfStatement, NodeIdentifier)
 
 cwd = os.path.abspath(os.path.dirname(__file__))
 DB_DIR = os.path.join(cwd, "../inputs")
@@ -115,3 +115,15 @@ def test_axiom_annotation(self):
             ):
                 ok1 = True
         assert ok1
+
+    def test_node_prefixes(self):
+        session = self.session
+        n = 0
+        for row in session.query(NodeIdentifier).filter(
+            NodeIdentifier.prefix == "RO"
+        ):
+            logging.info(row)
+            n += 1
+            assert row.id.startswith("RO:")
+            self.assertEqual(row.id, row.prefix + ":" + row.local_identifier)
+

From 3132bcec0bfc5e6e319c1229ab828ec0a7d9ef52 Mon Sep 17 00:00:00 2001
From: cmungall <cjm@berkeleybop.org>
Date: Sat, 17 Dec 2022 12:36:13 -0800
Subject: [PATCH 2/2] lint

---
 tests/test_orm/test_basic_sqla.py | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/tests/test_orm/test_basic_sqla.py b/tests/test_orm/test_basic_sqla.py
index e305013..80808a1 100644
--- a/tests/test_orm/test_basic_sqla.py
+++ b/tests/test_orm/test_basic_sqla.py
@@ -5,8 +5,9 @@
 from sqlalchemy import create_engine
 from sqlalchemy.orm import aliased, sessionmaker
 
-from semsql.sqla.semsql import (OwlAxiomAnnotation, OwlSomeValuesFrom,
-                                RdfsLabelStatement, RdfsSubclassOfStatement, NodeIdentifier)
+from semsql.sqla.semsql import (NodeIdentifier, OwlAxiomAnnotation,
+                                OwlSomeValuesFrom, RdfsLabelStatement,
+                                RdfsSubclassOfStatement)
 
 cwd = os.path.abspath(os.path.dirname(__file__))
 DB_DIR = os.path.join(cwd, "../inputs")
@@ -119,11 +120,8 @@ def test_axiom_annotation(self):
     def test_node_prefixes(self):
         session = self.session
         n = 0
-        for row in session.query(NodeIdentifier).filter(
-            NodeIdentifier.prefix == "RO"
-        ):
+        for row in session.query(NodeIdentifier).filter(NodeIdentifier.prefix == "RO"):
             logging.info(row)
             n += 1
             assert row.id.startswith("RO:")
             self.assertEqual(row.id, row.prefix + ":" + row.local_identifier)
-
