From bab8c694fd913f9b25e1970805d438e0f9c90d52 Mon Sep 17 00:00:00 2001
From: Damien Goutte-Gattat <dpg44@cam.ac.uk>
Date: Tue, 15 Oct 2024 15:57:44 +0100
Subject: [PATCH 1/2] Filter out dangling gene IRIs.

When compiling the merged import module, make sure to filter out IRIs
from <http://www,ncbi.nlm.nih.gov/gene/> and
<http://birdgenenames.org/>, which otherwise end up as dangling classes
under owl:Thing.
---
 src/ontology/Makefile        | 4 ++--
 src/ontology/uberon-odk.yaml | 2 ++
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/ontology/Makefile b/src/ontology/Makefile
index 0a17b5cf5..b127efc0a 100644
--- a/src/ontology/Makefile
+++ b/src/ontology/Makefile
@@ -10,7 +10,7 @@
 # More information: https://github.com/INCATools/ontology-development-kit/
 
 # Fingerprint of the configuration file when this Makefile was last generated
-CONFIG_HASH=                943829f9eb8e1b8d46bf5f3f878364bb18f10e0d9eee11d7c28bfb3dfba894c7
+CONFIG_HASH=                0a0a5c4407603e3386ecd7b01d03996f6e25afe375d62acd1943b88594d42c2e
 
 
 # ----------------------------------------
@@ -391,7 +391,7 @@ $(IMPORTDIR)/merged_terms_combined.txt: $(ALL_TERMS_COMBINED)
 
 $(IMPORTDIR)/merged_import.owl: $(MIRRORDIR)/merged.owl $(IMPORTDIR)/merged_terms_combined.txt
 	if [ $(IMP) = true ]; then $(ROBOT) merge -i $< \
-		remove  --select "<http://www.informatics.jax.org/marker/MGI:*>" remove  --select "<http://purl.obolibrary.org/obo/OBA_*>" remove  --select "<http://purl.obolibrary.org/obo/ENVO_*>" remove  --select "<http://purl.obolibrary.org/obo/OBI_*>" remove  --select "<http://purl.obolibrary.org/obo/GOCHE_*>" remove  --select "<http://www.genenames.org/cgi-bin/gene_symbol_report*>"  \
+		remove  --select "<http://www.informatics.jax.org/marker/MGI:*>" remove  --select "<http://purl.obolibrary.org/obo/OBA_*>" remove  --select "<http://purl.obolibrary.org/obo/ENVO_*>" remove  --select "<http://purl.obolibrary.org/obo/OBI_*>" remove  --select "<http://purl.obolibrary.org/obo/GOCHE_*>" remove  --select "<http://www.genenames.org/cgi-bin/gene_symbol_report*>" remove  --select "<http://www.ncbi.nlm.nih.gov/gene/*>" remove  --select "<http://birdgenenames.org/cgnc/GeneReport?id=*>"  \
 		extract -T $(IMPORTDIR)/merged_terms_combined.txt --force true --copy-ontology-annotations true --individuals exclude --method BOT \
 		remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) -T $(IMPORTDIR)/merged_terms_combined.txt --select complement --select annotation-properties \
 		query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \
diff --git a/src/ontology/uberon-odk.yaml b/src/ontology/uberon-odk.yaml
index 7fe47e44b..8fe7a465f 100644
--- a/src/ontology/uberon-odk.yaml
+++ b/src/ontology/uberon-odk.yaml
@@ -42,6 +42,8 @@ import_group:
     - <http://purl.obolibrary.org/obo/OBI_*>
     - <http://purl.obolibrary.org/obo/GOCHE_*>
     - <http://www.genenames.org/cgi-bin/gene_symbol_report*>
+    - <http://www.ncbi.nlm.nih.gov/gene/*>
+    - <http://birdgenenames.org/cgnc/GeneReport*>
   products:
     - id: pr
       make_base: TRUE

From 56940457d923af5ff72db0fb24bcc2b9a81a8521 Mon Sep 17 00:00:00 2001
From: Damien Goutte-Gattat <dpg44@cam.ac.uk>
Date: Tue, 15 Oct 2024 16:16:20 +0100
Subject: [PATCH 2/2] Commit re-generated Makefile.

---
 src/ontology/Makefile | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/ontology/Makefile b/src/ontology/Makefile
index b127efc0a..1da07760e 100644
--- a/src/ontology/Makefile
+++ b/src/ontology/Makefile
@@ -10,7 +10,7 @@
 # More information: https://github.com/INCATools/ontology-development-kit/
 
 # Fingerprint of the configuration file when this Makefile was last generated
-CONFIG_HASH=                0a0a5c4407603e3386ecd7b01d03996f6e25afe375d62acd1943b88594d42c2e
+CONFIG_HASH=                60e47a069bd32a71a48c480dcf88b75d116c5eef7d1f9a55073500ff79968b28
 
 
 # ----------------------------------------
@@ -391,7 +391,7 @@ $(IMPORTDIR)/merged_terms_combined.txt: $(ALL_TERMS_COMBINED)
 
 $(IMPORTDIR)/merged_import.owl: $(MIRRORDIR)/merged.owl $(IMPORTDIR)/merged_terms_combined.txt
 	if [ $(IMP) = true ]; then $(ROBOT) merge -i $< \
-		remove  --select "<http://www.informatics.jax.org/marker/MGI:*>" remove  --select "<http://purl.obolibrary.org/obo/OBA_*>" remove  --select "<http://purl.obolibrary.org/obo/ENVO_*>" remove  --select "<http://purl.obolibrary.org/obo/OBI_*>" remove  --select "<http://purl.obolibrary.org/obo/GOCHE_*>" remove  --select "<http://www.genenames.org/cgi-bin/gene_symbol_report*>" remove  --select "<http://www.ncbi.nlm.nih.gov/gene/*>" remove  --select "<http://birdgenenames.org/cgnc/GeneReport?id=*>"  \
+		remove  --select "<http://www.informatics.jax.org/marker/MGI:*>" remove  --select "<http://purl.obolibrary.org/obo/OBA_*>" remove  --select "<http://purl.obolibrary.org/obo/ENVO_*>" remove  --select "<http://purl.obolibrary.org/obo/OBI_*>" remove  --select "<http://purl.obolibrary.org/obo/GOCHE_*>" remove  --select "<http://www.genenames.org/cgi-bin/gene_symbol_report*>" remove  --select "<http://www.ncbi.nlm.nih.gov/gene/*>" remove  --select "<http://birdgenenames.org/cgnc/GeneReport*>"  \
 		extract -T $(IMPORTDIR)/merged_terms_combined.txt --force true --copy-ontology-annotations true --individuals exclude --method BOT \
 		remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) -T $(IMPORTDIR)/merged_terms_combined.txt --select complement --select annotation-properties \
 		query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \