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Deals with user request in #9579

src/ontology/build-without-imports.sh

@@ -5,4 +5,5 @@ set -e
 sh run.sh make hpoa_clean -B
 test tmp/hpoa/hpo-annotation-data/README.md
 sh run.sh make IMP=false prepare_release -B
-sh run.sh make hpoa -B
+sh run.sh make hpoa -B
+sh run.sh make hpo_diff -B

src/ontology/hp.Makefile

@@ -247,12 +247,19 @@ hpo_jar: .FORCE
 	wget https://github.com/Phenomics/ontodiff/releases/download/$(HPODIFFVERSION)/hpodiff.jar -O $(HPODIFFJAR)
 
 # The new version is the version that was just created by the release
+
+#HPO_NEW_DIFF=http://purl.obolibrary.org/obo/hp/releases/2022-12-15/hp.obo
+HPO_OLD_DIFF=http://purl.obolibrary.org/obo/hp.obo
+
 tmp/$(ONT).obo.new:
 	cp ../../$(ONT).obo $@
 
+#tmp/$(ONT).obo.new:
+#	wget "$(HPO_NEW_DIFF)" -O $@
+
 # The old version is the version that is currently published
 tmp/$(ONT).obo.old: .FORCE
-	wget http://purl.obolibrary.org/obo/hp.obo -O $@
+	wget "$(HPO_OLD_DIFF)" -O $@
 
 # As said before, we create this dummy file (reports/hpo_nice_diff.md) that will
 # simply list all previously created reports that are copied into the reports folder
@@ -261,9 +268,8 @@ hpo_diff: hpo_jar tmp/$(ONT).obo.new tmp/$(ONT).obo.old
 	java -jar $(HPODIFFJAR) tmp/$(ONT).obo.new tmp/$(ONT).obo.old
 	cp tmp/hpodiff*.xlsx reports
 
-
-tmp/hp-build.owl:
-	wget https://ci.monarchinitiative.org/view/pipelines/job/hpo-pipeline-dev2/lastSuccessfulBuild/artifact/hp-full.owl -O $@
+#tmp/hp-build.owl:
+#	wget https://ci.monarchinitiative.org/view/pipelines/job/hpo-pipeline-dev2/lastSuccessfulBuild/artifact/hp-full.owl -O $@
 
 tmp/patternised_classes.txt: patternised_classes.txt
 	cp $< $@

src/ontology/reports/autoimmune-antibody-report.tsv

@@ -230,7 +230,7 @@
 <http://purl.obolibrary.org/obo/HP_5000015>	"Anti-Homer-3 antibody"	"The presence of autoantibodies (immunoglobulins) in the blood circulation that react against Homer-3."	"PMID:26377085"	"Anti-Homer protein homolog 3 antibody"
 <http://purl.obolibrary.org/obo/HP_4000020>	"Anti-BP180 antibody positivity"	"Bullous pemphigoid (BP) is an autoimmune disease associated with subepidermal blistering due to autoantibodies directed against BP180 and BP230. BP180 is currently considered as the major pathogenic autoantigen."	"PMID:32048350"	
 <http://purl.obolibrary.org/obo/HP_4000024>	"Anti-laminin antibody positivity"	"The presence of autoantibodies (immunoglobulins) in the serum that react against a laminin. Laminins are major components of the basement membrane."		
-<http://purl.obolibrary.org/obo/HP_5000022>	"Anti-Ma2 antibody positivity"	"The presence of autoantibodies (immunoglobulins) in the blood circulation that react against Ma2."	"PMID:26664526|PMID:15179063|PMID:18223018|PMID:31454760|PMID:31044049|PMID:15215214|PMID:27460184"	"Anti-Ta antibody"
+<http://purl.obolibrary.org/obo/HP_5000022>	"Anti-Ma2 antibody positivity"	"The presence of autoantibodies (immunoglobulins) in the blood circulation that react against Ma2."	"PMID:31044049|PMID:27460184|PMID:15215214|PMID:15179063|PMID:18223018|PMID:31454760|PMID:26664526"	"Anti-Ta antibody"
 <http://purl.obolibrary.org/obo/HP_0034116>	"Anti-thyrotropin receptor antibody"	"The presence of autoantibodies (immunoglobulins) in the blood circulation that react against thyrotropin receptor antibody."	"PMID:32459722"	
 <http://purl.obolibrary.org/obo/HP_0031810>	"Anti-ganglioside antibody positivity"	"The presence of autoantibodies (immunoglobulins) in the serum that react to gangliosides."	"PMID:8027366"	
 <http://purl.obolibrary.org/obo/HP_0034017>	"Anti-class I HLA antibody positivity"	"The presence of autoantibodies (immunoglobulins) in the blood circulation that react against a class I human leukocyte antigen (HLA). Class I HLA corresponds to MHC class I (A, B, and C)."