Update HPO release files

obophenotype · Aug 13, 2024 · b998512 · b998512
1 parent 1b7b845
commit b998512
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Showing 57 changed files with 53,505 additions and 15,009 deletions.
diff --git a/hp-base.owl b/hp-base.owl
diff --git a/hp.obo b/hp.obo
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/2024-07-01/patterns/definitions.owl>
-Annotation(owl:versionInfo "2024-07-01")
+<http://purl.obolibrary.org/obo/hp/releases/2024-08-13/patterns/definitions.owl>
+Annotation(owl:versionInfo "2024-08-13")
 
 
 

diff --git a/src/ontology/Makefile b/src/ontology/Makefile
@@ -1,7 +1,7 @@
 # ----------------------------------------
 # Makefile for hp
 # Generated using ontology-development-kit
-# ODK Version: v1.5.1
+# ODK Version: v1.6
 # ----------------------------------------
 # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use hp.Makefile instead
 
@@ -46,7 +46,7 @@ REPORT_PROFILE_OPTS =
 OBO_FORMAT_OPTIONS =        
 SPARQL_VALIDATION_CHECKS =  equivalent-classes owldef-self-reference synonym_ends_with_illegal_character deprecated_class_reference iri-range label-with-iri taxon-range double-space illegal-synonym-type deprecated-consider illegal-annotation-property orcid-contributor orcid-xref-is-not-formatted-correctly xref-uses-unknown-prefix noparent nolabels missing-parent-hpo primary-label-translation-tag self-reference 
 SPARQL_EXPORTS =            basic-report xrefs synonyms layperson-synonyms autoimmune-antibody-report hp-attribution-report 
-ODK_VERSION_MAKEFILE =      v1.5.1
+ODK_VERSION_MAKEFILE =      v1.6
 
 TODAY ?=                    $(shell date +%Y-%m-%d)
 OBODATE ?=                  $(shell date +'%d:%m:%Y %H:%M')

diff --git a/src/ontology/imports/merged_import.owl b/src/ontology/imports/merged_import.owl
diff --git a/src/ontology/reports/autoimmune-antibody-report.tsv b/src/ontology/reports/autoimmune-antibody-report.tsv
@@ -32,6 +32,7 @@
 <http://purl.obolibrary.org/obo/HP_5000036>	"Anti-TRIM9/TRIM67 antibody"	"The presence of autoantibodies (immunoglobulins) in the blood circulation that react against TRIM9/TRIM67."	"PMID:30350014"	
 <http://purl.obolibrary.org/obo/HP_0034137>	"Anti-contactin-1 antibody positivity"	"The presence of autoantibodies (immunoglobulins) in the blood circulation that react against CNTN1."	"PMID:32266541|PMID:34675937"	"Anti-CNTN1 antibody positivity"
 <http://purl.obolibrary.org/obo/HP_6000496>	"Anti-factor X antibody positivity"	"The presence of an antibody in the blood circulation that is directed against factor X."	"PMID:24074948"	"Anti-FX antibody positivity"
+<http://purl.obolibrary.org/obo/HP_6001061>	"Anti-apolipoprotein CII autoantibody positivity"	"The presence of autoantibodies in the blood circulation that react against apoCII."	"PMID:30706594"	"Anti-apoCII autoantibody positivity"
 <http://purl.obolibrary.org/obo/HP_0033593>	"Anti-H2A-H2B antibody positivity"	"The presence of autoantibodies in the blood circulation that react against the H2A-H2B histone dimer."	"PMID:7986226"	
 <http://purl.obolibrary.org/obo/HP_0034189>	"Anti-thyroid-stimulating hormone receptor antibody positivity"	"The presence of autoantibodies (immunoglobulins) in the serum that react against thyroid-stimulating hormone."	"PMID:10874533|PMID:26293122|PMID:3018097|PMID:30224035|PMID:32459722"	"TRAbs|Anti-thyrotropin receptor antibody|Anti-TSH receptor antibody positivity"
 <http://purl.obolibrary.org/obo/HP_6000643>	"Anti-lamin A antibody positivity"	"The presence of autoantibodies (immunoglobulins) in the blood circulation that react against lamin A."	"PMID:1959878|PMID:2271902"	"Prelamin A antibody positivity|LMNA antibody positivity|PCNA antibody positivity|ki-67 antibody positivity"
@@ -171,6 +172,7 @@
 <http://purl.obolibrary.org/obo/HP_0034108>	"Anti-Y-box protein-1 antibody positivity"	"The presence of autoantibodies (immunoglobulins) in the blood circulation that react against Y-box protein-1."	"PMID:29554146"	"Anti-YB 1 antibody positivity"
 <http://purl.obolibrary.org/obo/HP_4000023>	"Anti-laminin gamma1 antibody positivity"	"The presence of autoantibodies (immunoglobulins) in the serum that react against laminin gamma-1."	"PMID:24154702"	
 <http://purl.obolibrary.org/obo/HP_6000193>	"Anti-osteoprotegerin antibody positivity"	"The presence of autoantibodies (immunoglobulins) in the blood circulation that react against osteoprotegerin."	"PMID:19812402|PMID:26092508|PMID:28534161"	"Anti-OPG antibody positivity"
+<http://purl.obolibrary.org/obo/HP_0025762>	"Anti-ganglionic acetylcholine receptor antibody positivity"	"The presence of autoantibodies (immunoglobulins) in the blood circulation that react against acetylcholine receptors of the ganglionic type."	"PMID:18474849"	
 <http://purl.obolibrary.org/obo/HP_0033554>	"Anti-Mi2 antibody positivity"	"The presence of autoantibodies in the blood circulation that react against the Mi-2 antigen."	"PMID:30938432"	
 <http://purl.obolibrary.org/obo/HP_0033563>	"Anti-tissue transglutaminase antibody positivity"	"The presence of autoantibodies (immunoglobulins) in the serum that react against tissue transglutaminase."	"PMID:33259121"	"Anti-tTG antibody positivity"
 <http://purl.obolibrary.org/obo/HP_0034081>	"Anti-Th/To antibody positivity"	"The presence of autoantibodies (immunoglobulins) in the blood circulation that react against Th/To."	"PMID:30316987"	
@@ -179,10 +181,12 @@
 <http://purl.obolibrary.org/obo/HP_0034148>	"Anti-isoleucyl tRNA-synthetase antibody positivity"	"The presence of autoantibodies (immunoglobulins) in the blood circulation that react against isoleucyl tRNA-synthetase."	"PMID:33343724"	"Anti-OJ antibody positivity"
 <http://purl.obolibrary.org/obo/HP_0034065>	"Anti-Zinc transporter 8 antibody positivity"	"The presence of autoantibodies (immunoglobulins) in the serum that react against zinc transporter 8."	"PMID:32946793"	"Anti ZnT8 autoantibodies"
 <http://purl.obolibrary.org/obo/HP_5000001>	"Anti-AMPAR antibody positivity"	"The presence of autoantibodies (immunoglobulins) in the blood circulation that react against anti-alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR)."	"PMID:25979696|PMID:29225271"	"Anti-alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor antibody"
+<http://purl.obolibrary.org/obo/HP_6001058>	"Anti-neuronal intermediate filament antibody positivity"	"The presence of autoantibodies (immunoglobulins) in the blood circulation that react against neuronal intermediate filament."	"PMID:30282771"	
 <http://purl.obolibrary.org/obo/HP_0033592>	"Anti-H3-H4 antibody positivity"	"The presence of autoantibodies in the blood circulation that react against the H3-H4 histone dimer."	"PMID:1864977|PMID:3874029|PMID:7986226"	
 <http://purl.obolibrary.org/obo/HP_0034062>	"Anti-insulin antibody positivity"	"The presence of autoantibodies (immunoglobulins) in the serum that react against insulin."	"PMID:17143785"	"Insulin autoantibodies|IAA positivity"
 <http://purl.obolibrary.org/obo/HP_0033629>	"IgG4 autoimmune antibody positivity"	"The presence of an antibody of subclass IgG4 in the blood circulation that is directed against the organism's own cells or tissues."	"PMID:29483905"	
 <http://purl.obolibrary.org/obo/HP_0034055>	"Anti-side-chain cleavage enzyme antibody positivity"	"The presence of autoantibodies (immunoglobulins) in the serum that react against cytochrome P450 cholesterol side-chain cleavage enzyme (P450scc), which is encoded by CYP11A1 cytochrome P450 family 11 subfamily A member 1 (Gene ID:1583)."	"PMID:9030872"	"Anti-P450scc"
+<http://purl.obolibrary.org/obo/HP_6001064>	"Anti-acetylcholine receptor antibody positivity"	"The presence of autoantibodies (immunoglobulins) in the blood circulation that react against acetylcholine receptor."	"PMID:18474849"	
 <http://purl.obolibrary.org/obo/HP_0030209>	"Calcium channel antibody positivity"	"The presence of autoantibodies (immunoglobulins) in the serum that react against voltage-gated calcium channels."	"PMID:7739683"	"Ca2+ channel antibody positivity|Ca channel antibody positivity"
 <http://purl.obolibrary.org/obo/HP_5000007>	"Anti-DPPX antibody"	"The presence of autoantibodies (immunoglobulins) in the blood circulation that react against dipeptidyl-peptidase-like protein 6 (DPPX)."	"PMID:27299786|PMID:28258082|PMID:32087460"	"Anti-dipeptidyl-peptidase-like protein 6 antibody"
 <http://purl.obolibrary.org/obo/HP_0034133>	"Anti-GM3 antibody positivity"	"The presence of autoantibodies (immunoglobulins) in the blood circulation that react against ganglioside GM3."	"PMID:34174799"	
@@ -213,6 +217,7 @@
 <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_6001060>	"Anti-lipoprotein lipase autoantibody positivity"	"The presence of autoantibodies (immunoglobulins) in the blood circulation that react against anti-lipoprotein lipase."	"PMID:15840743|PMID:28916403|PMID:29784574|PMID:36123759"	"Anti-LPL autoantibody positivity"
 <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"	
@@ -236,9 +241,11 @@
 <http://purl.obolibrary.org/obo/HP_0034157>	"Anti-beta-2-Glycoprotein I IgM antibody positivity"	"Presence of IgM antibodies against beta 2 glycoprotein I in the circulation. Beta-2 glycoprotein I (beta2GPI) is the principal target of autoantibodies in the antiphospholipid syndrome."	"PMID:33957795|PMID:34218350"	"Anti-beta2GPI IgM antibody positivity"
 <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_5000022>	"Anti-Ma2 antibody positivity"	"The presence of autoantibodies (immunoglobulins) in the blood circulation that react against Ma2."	"PMID:15179063|PMID:15215214|PMID:18223018|PMID:26664526|PMID:27460184|PMID:31044049|PMID:31454760"	"Anti-Ta antibody"
+<http://purl.obolibrary.org/obo/HP_6001015>	"Anti-HLA-DQ antibody positivity"	"The presence of autoantibodies (immunoglobulins) in the blood circulation that react against a human leukocyte antigen (HLA-DQ). DQ is one of several antigens involved in antibody-mediated rejection of organ transplants."	"PMID:23260706"	
 <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_0033555>	"Anti-Ro/SS-A antibody positivity"	"The presence of autoantibodies in the blood circulation that react against Ro/SSA autoantigens."	"PMID:1522616|PMID:15804706"	"Anti-Ro/SSA antibody positivity"
 <http://purl.obolibrary.org/obo/HP_5000025>	"Anti-mGluR5 antibody"	"The presence of autoantibodies (immunoglobulins) in the blood circulation that react against metabotropic glutamate receptor 5 (mGluR5)."	"PMID:29703767"	"Anti-Metabotropic Glutamate Receptor Type 5 antibody"
+<http://purl.obolibrary.org/obo/HP_6001059>	"Anti-DREBRIN antibody positivity"	"The presence of autoantibodies in the serum that react against dendritic spine scaffolding protein Drebrin."	"PMID:32196746"	
 <http://purl.obolibrary.org/obo/HP_0033560>	"Anti-PM-Scl antibody positivity"	"Anti-PM-Scl antibodies target components of RNA-processing exosome complex in the nucleolus. There are ten proteins in this complex and antibodies to eight of them are found at varying frequencies; PM/Scl-100, PM/Scl-75, hRrp4, hRrp42, hRrp46, hCs14, hRrp41, and hRrp40."	"PMID:17643929"	"Anti-PM/Scl antibody positivity"
 <http://purl.obolibrary.org/obo/HP_0034124>	"Anti-GD1b antibody positivity"	"The presence of autoantibodies (immunoglobulins) in the blood circulation that react against GD1b ganglioside."	"PMID:31837178"	
 <http://purl.obolibrary.org/obo/HP_0034155>	"Anti-sp100 antibody positivity"	"The presence of autoantibodies (immunoglobulins) in the serum that react against sp100. Autoantibodies causing the MND pattern are directed against sp100, sp140, promyelocytic leukemia nuclear body proteins (PML) or ubiquitin-like modifier (SUMO) proteins, while in the punctate nuclear envelope pattern, the target antigens are gp210, nucleoporin-62 or laminin B receptor proteins."	"PMID:32286240|PMID:33789734"