Merge pull request #10436 from obophenotype/release04042024

Update release files 04.04.2024 (Hotfix release)
obophenotype · Apr 4, 2024 · 008b03d · 008b03d
2 parents fd279fa + 19cd98f
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diff --git a/hp-base.owl b/hp-base.owl
diff --git a/hp.obo b/hp.obo
@@ -1,5 +1,5 @@
 format-version: 1.2
-data-version: hp/releases/2024-04-03
+data-version: hp/releases/2024-04-04
 subsetdef: hposlim_core "Core clinical terminology"
 subsetdef: secondary_consequence "Consequence of a disorder in another organ system."
 synonymtypedef: abbreviation "abbreviation"
@@ -21,7 +21,7 @@ property_value: http://purl.org/dc/elements/1.1/subject "Phenotypic abnormalitie
 property_value: http://purl.org/dc/elements/1.1/title "Human Phenotype Ontology" xsd:string
 property_value: http://purl.org/dc/terms/license https://hpo.jax.org/app/license
 property_value: IAO:0000700 HP:0000001
-property_value: owl:versionInfo "2024-04-03" xsd:string
+property_value: owl:versionInfo "2024-04-04" xsd:string
 logical-definition-view-relation: has_part
 
 [Term]
@@ -189826,10 +189826,10 @@ property_value: IAO:0000233 https://github.com/obophenotype/human-phenotype-onto
 
 [Term]
 id: HP:6000380
-name: CHANGE ME
-def: "A pulmonary cavity is a gas-filled area of the lung in the center of a nodule or area of consolidation and may be clinically observed by use of plain chest radiography or computed tomography. Cavities are present in a wide variety of infectious and noninfectious processes." [PMID:18400799]
-is_a: HP:0000357 ! Abnormal location of ears
-property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0736-9199
+name: Anti-perilipin-1 antibody positivity
+def: "The presence of autoantibodies in the serum that react against perilipin-1 (PLIN1)." [PMID:30283460, PMID:35709010, PMID:35771980, PMID:36538601]
+is_a: HP:0030057 ! Autoimmune antibody positivity
+property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-3387-1836
 property_value: IAO:0000233 https://github.com/obophenotype/human-phenotype-ontology/issues/8972
 
 [Term]
@@ -192517,6 +192517,102 @@ synonym: "Reduced long-acting natriuretic peptide concentration" EXACT []
 is_a: HP:0010876 ! Abnormal circulating protein concentration
 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0736-9199
 
+[Term]
+id: HP:6000694
+name: Elevated circulating 1-pyrroline-5-carboxylic acid acid concentration
+def: "The concentration of delta-1-pyrroline-5-carboxylate in the blood circulation is above the upper limit of normal." [PMID:9700195]
+synonym: "Elevated circulating delta-1-pyrroline-5-carboxylate concentration" EXACT []
+is_a: HP:0010996 ! Abnormal circulating monocarboxylic acid concentration
+property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0736-9199
+property_value: IAO:0000233 https://github.com/obophenotype/human-phenotype-ontology/issues/8289
+
+[Term]
+id: HP:6000695
+name: Reduced tissue delta-1-pyrroline-5-carboxylate dehydrogenase activity
+def: "Concentration or activity of delta-1-pyrroline-5-carboxylate dehydrogenase (P5CDH; EC 1.5.1.12) below the lower limit of normal. P5CDH can be measured in multiple tissues including leukocytes and cultured fibroblasts. P5CDH is a mitochondrial matrix NAD(+)-dependent dehydrogenase which catalyzes the second step of the proline degradation pathway, converting pyrroline-5-carboxylate to glutamate." [PMID:2624476]
+is_a: HP:6000231 ! Abnormal tissue enzyme concentration or activity
+property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0736-9199
+property_value: IAO:0000233 https://github.com/obophenotype/human-phenotype-ontology/issues/8290
+
+[Term]
+id: HP:6000696
+name: Elevated circulating N-carbamyl-beta-aminoisobutyric acid concentration
+def: "The concentration of N-carbamyl-beta-aminoisobutyric acid in the blood circulation is above the upper limit of normal." [PMID:15385443]
+is_a: HP:0010996 ! Abnormal circulating monocarboxylic acid concentration
+property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0736-9199
+property_value: IAO:0000233 https://github.com/obophenotype/human-phenotype-ontology/issues/8293
+
+[Term]
+id: HP:6000697
+name: Low tissue ferrochelatase activity
+def: "Concentration or activity of Ferrochelatase (FECH; EC 4.99.1.1) below the lower limit of normal. FECH enzyme can be measured in multiple tissues including leukocytes and cultured fibroblasts. FECH is the terminal enzyme of the heme biosynthetic pathway, and catalyzes the insertion of iron into protoporphyrin to form heme." [PMID:8571955]
+is_a: HP:6000231 ! Abnormal tissue enzyme concentration or activity
+property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0736-9199
+property_value: IAO:0000233 https://github.com/obophenotype/human-phenotype-ontology/issues/8300
+
+[Term]
+id: HP:6000698
+name: Elevated circulating heptacarboxylporphyrin concentration
+def: "The concentration of heptacarboxylporphyrin in the blood circulation is above the upper limit of normal." [PMID:11929047]
+is_a: HP:0034606 ! Elevated circulating porphyrin concentration
+property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0736-9199
+property_value: IAO:0000233 https://github.com/obophenotype/human-phenotype-ontology/issues/8302
+
+[Term]
+id: HP:6000699
+name: Aggravated by menstruation
+def: "Applied to a sign or symptom that is more severe during mensutruation." [PMID:30523495, PMID:32966006]
+comment: Lipoprotein(a) [Lp(a)] is a macromolecular complex in human plasma which represents a quantitative genetic trait with a heritability of 0.7 or higher. High concentrations of Lp(a) are associated with atherothrombotic disease i.e. myocardial infarction, stroke, peripheral vascular disease and childhood thromboembolism. The covalent Lp(a) complex is assembled in plasma from low-density lipoprotein (LDL) and apolipoprotein(a), a plasminogen-related glycoprotein.
+is_a: HP:0025285 ! Aggravated by
+property_value: http://purl.org/dc/terms/contributor https://orcid.org/0009-0005-6714-5727
+property_value: IAO:0000233 https://github.com/obophenotype/human-phenotype-ontology/issues/8306
+
+[Term]
+id: HP:6000700
+name: Reduced breast milk zinc concentration
+def: "The concentration of zink in breast milk is below the lower limit of normal." [PMID:35230756]
+comment: Zinc is a normal component in human milk. One known cause is below-normal milk zinc levels due to maternal genetic mutations affecting mammary zinc transport proteins.
+is_a: HP:0032243 ! Abnormal tissue metabolite concentration
+property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0736-9199
+property_value: IAO:0000233 https://github.com/obophenotype/human-phenotype-ontology/issues/8361
+
+[Term]
+id: HP:6000701
+name: Elevated urinary bile acid level
+def: "The amount of bile acid in the urine, normalized for urine concentration, is above the upper limit of normal." []
+is_a: HP:0031980 ! Abnormal urine carboxylic acid level
+property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0736-9199
+property_value: IAO:0000233 https://github.com/obophenotype/human-phenotype-ontology/issues/8379
+
+[Term]
+id: HP:6000702
+name: Elevated urinary glyoxylic acid level
+def: "The amount of glyoxylic acid in the urine, normalized for urine concentration, is above the upper limit of normal. The conjugate base of glyoxylic acid is known as glyoxylate." [PMID:449695]
+synonym: "Elevated urinary alpha-ketoacetic acid level" EXACT []
+synonym: "Elevated urinary glyoxylate level" EXACT []
+synonym: "Elevated urinary oxoacetic acid level" EXACT []
+is_a: HP:0033303 ! Elevated urinary monocarboxylic acid level
+property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0736-9199
+property_value: IAO:0000233 https://github.com/obophenotype/human-phenotype-ontology/issues/8384
+
+[Term]
+id: HP:6000703
+name: Elevated circulating 3-hydroxyanthranilic acid concentration
+def: "The concentration of 3-hydroxyanthranilic acid in the blood circulation is above the upper limit of normal." [PMID:22084587]
+is_a: HP:0033108 ! Abnormal circulating proteinogenic amino acid derivative concentration
+property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0736-9199
+property_value: IAO:0000233 https://github.com/obophenotype/human-phenotype-ontology/issues/8405
+
+[Term]
+id: HP:6000704
+name: Elevated circulating CXCL9 concentration
+def: "The concentration of chemokine (C-X-C motif) ligand 9 in the blood circulation is above the upper limit of normal." [PMID:32060845]
+comment: CXCL9, also known as monokine induced by gamma-interferon (MIG), can be produced during inflammatory conditions by myeloid cells within the tumor microenvironment.
+synonym: "Elevated circulating monokine induced by gamma-interferon concentration" EXACT []
+is_a: HP:0011112 ! Abnormal circulating cytokine concentration
+property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0736-9199
+property_value: IAO:0000233 https://github.com/obophenotype/human-phenotype-ontology/issues/8413
+
 [Typedef]
 id: inheres_in
 name: inheres in

diff --git a/patterns/definitions.owl b/patterns/definitions.owl
@@ -7,8 +7,8 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/hp/patterns/definitions.owl>
-<http://purl.obolibrary.org/obo/hp/releases/2024-04-03/patterns/definitions.owl>
-Annotation(owl:versionInfo "2024-04-03")
+<http://purl.obolibrary.org/obo/hp/releases/2024-04-04/patterns/definitions.owl>
+Annotation(owl:versionInfo "2024-04-04")
 
 
 

diff --git a/src/ontology/hp.Makefile b/src/ontology/hp.Makefile
@@ -353,8 +353,42 @@ 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 $@
+##################
+### KGCL Diff ####
+##################
+
+KGCL_ONTOLOGY=hp-base.obo
+
+upgrade_oak:
+	pip install -U oaklib
+
+.PHONY: kgcl-diff
+kgcl-diff: kgcl-diff-release-base
+
+.PHONY: kgcl-diff-release-base
+kgcl-diff-release-base: reports/difference_release_base.yaml \
+						reports/difference_release_base.tsv \
+						reports/difference_release_base.md
+
+tmp/hp-released.obo:
+	wget http://purl.obolibrary.org/obo/hp.obo -O tmp/hp-released.obo
+
+reports/difference_release_base.md: tmp/hp-released.obo $(KGCL_ONTOLOGY)
+	runoak -i simpleobo:tmp/hp-released.obo diff -X simpleobo:$(KGCL_ONTOLOGY) -o $@ --output-type md
+
+reports/difference_release_base.tsv: tmp/hp-released.obo $(KGCL_ONTOLOGY)
+	runoak -i simpleobo:tmp/hp-released.obo diff -X simpleobo:$(KGCL_ONTOLOGY) \
+	-o $@ --output-type csv --statistics --group-by-property oio:hasOBONamespace
+
+reports/difference_release_base.txt: tmp/hp-released.obo $(KGCL_ONTOLOGY)
+	runoak -i simpleobo:tmp/hp-released.obo diff -X simpleobo:$(KGCL_ONTOLOGY) -o $@ --output-type kgcl
+
+reports/difference_release_base.yaml: tmp/hp-released.obo $(KGCL_ONTOLOGY)
+	runoak -i simpleobo:tmp/hp-released.obo diff -X simpleobo:$(KGCL_ONTOLOGY) -o $@ --output-type yaml
+
+########################
+### DOSDP workflows ####
+########################
 
 tmp/patternised_classes.txt: patternised_classes.txt
 	cp $< $@
@@ -578,32 +612,3 @@ $(TMPDIR)/hp-%-merged.owl: hp-base.owl tmp/%.owl
 mappings: 
 	$(MAKE_FAST) ../mappings/hp-snomed.lexmatch.sssom.tsv
 
-##################
-### KGCL Diff ####
-##################
-
-.PHONY: kgcl-diff
-kgcl-diff: kgcl-diff-release-base
-
-.PHONY: kgcl-diff-md-release-base kgcl-diff-table-release-base kgcl-diff-txt-release-base kgcl-diff-yaml-release-base 
-kgcl-diff-md-release-base: reports/difference_release_base.md
-kgcl-diff-table-release-base: reports/difference_release_base.tsv
-kgcl-diff-txt-release-base: reports/difference_release_base.txt
-kgcl-diff-yaml-release-base: reports/difference_release_base.yaml
-kgcl-diff-release-base: kgcl-diff-md-release-base kgcl-diff-table-release-base kgcl-diff-txt-release-base kgcl-diff-yaml-release-base
-
-tmp/hp-released.obo:
-	wget http://purl.obolibrary.org/obo/hp.obo -O tmp/hp-released.obo
-
-reports/difference_release_base.md: tmp/hp-released.obo hp.obo
-	runoak -i simpleobo:tmp/hp-released.obo diff -X simpleobo:hp.obo -o $@ --output-type md
-
-reports/difference_release_base.tsv: tmp/hp-released.obo hp.obo
-	runoak -i simpleobo:tmp/hp-released.obo diff -X simpleobo:hp.obo \
-	-o $@ --output-type csv --statistics --group-by-property oio:hasOBONamespace
-
-reports/difference_release_base.txt: tmp/hp-released.obo hp.obo
-	runoak -i simpleobo:tmp/hp-released.obo diff -X simpleobo:hp.obo -o $@ --output-type kgcl
-
-reports/difference_release_base.yaml: tmp/hp-released.obo hp.obo
-	runoak -i simpleobo:tmp/hp-released.obo diff -X simpleobo:hp.obo -o $@ --output-type yaml
diff --git a/src/ontology/reports/autoimmune-antibody-report.tsv b/src/ontology/reports/autoimmune-antibody-report.tsv
@@ -204,6 +204,7 @@
 <http://purl.obolibrary.org/obo/HP_6000497>	"Anti-factor XI antibody positivity"	"The presence of an antibody in the blood circulation that is directed against factor XI."	"PMID:18519152"	"Anti-FXI antibody positivity"
 <http://purl.obolibrary.org/obo/HP_0032469>	"Anti-asialoglycoprotein receptor antibody positivity"	"Presence of autoantibodies against the asialoglycoprotein receptor (ASGPR) in the blood circulation."	"PMID:26000135"	
 <http://purl.obolibrary.org/obo/HP_5000026>	"Anti-neurexin-3alpha antibody positivity"	"The presence of autoantibodies (immunoglobulins) in the blood circulation that react against neurexin-3alpha."	"PMID:27170572|PMID:27170573|PMID:28840178"	"Anti-neurexin-3alpha antibody"
+<http://purl.obolibrary.org/obo/HP_6000380>	"Anti-perilipin-1 antibody positivity"	"The presence of autoantibodies in the serum that react against perilipin-1 (PLIN1)."	"PMID:30283460|PMID:35709010|PMID:35771980|PMID:36538601"	
 <http://purl.obolibrary.org/obo/HP_6000187>	"Anti-thrombospondin type I domain-containing 7A antibody positivity"	"The presence of autoantibodies (immunoglobulins) in the blood circulation that react against thrombospondin type I domain-containing 7A."	"PMID:35564696"	"Anti-THSD7A antibody present in blood|Anti-THSD7A antibody"
 <http://purl.obolibrary.org/obo/HP_0033559>	"Anti-myeloperoxidase antibody positivity"	"The presence of autoantibodies in the blood circulation that react against myeloperoxidase."	"PMID:30767872"	"Anti-MPO antibody positivity|Anti-myeloperoxidase specific antineutrophil cytoplasmic antibody|MPO-ANCA"
 <http://purl.obolibrary.org/obo/HP_0033038>	"Anti-RNA-polymerase-III-autoantibody positivity"	"The presence of autoantibodies in the serum that react to RNA-polymerase III."	"PMID:31858335"