Merge pull request #10972 from obophenotype/release20250116

Update Release files for January HPO release
obophenotype · Jan 16, 2025 · 6376ce5 · 6376ce5
2 parents 25523a8 + 56adddf
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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/2024-12-12
+data-version: hp/releases/2025-01-16
 subsetdef: hposlim_core "Core clinical terminology"
 subsetdef: secondary_consequence "Consequence of a disorder in another organ system."
 synonymtypedef: abbreviation "abbreviation"
@@ -23,7 +23,7 @@ property_value: dc:rights "Peter Robinson, Sebastian Koehler, The Human Phenotyp
 property_value: dc:subject "Phenotypic abnormalities encountered in human disease" xsd:string
 property_value: dc:title "Human Phenotype Ontology" xsd:string
 property_value: IAO:0000700 HP:0000001
-property_value: owl:versionInfo "2024-12-12" xsd:string
+property_value: owl:versionInfo "2025-01-16" xsd:string
 property_value: terms:license https://hpo.jax.org/app/license
 logical-definition-view-relation: has_part
 
@@ -3008,6 +3008,7 @@ name: Facial edema
 synonym: "Facial oedema" EXACT uk_spelling []
 synonym: "Facial puffiness" EXACT layperson [https://orcid.org/0000-0001-5889-4463]
 synonym: "Facial swelling" EXACT layperson [https://orcid.org/0000-0001-5889-4463]
+synonym: "Swelling of the face" EXACT []
 xref: SNOMEDCT_US:445088006
 xref: UMLS:C0542571
 is_a: HP:0000969 ! Edema
@@ -14023,6 +14024,7 @@ is_a: HP:0006561 ! Lipid accumulation in hepatocytes
 [Term]
 id: HP:0001399
 name: Hepatic failure
+synonym: "Hepatic insufficiency" EXACT []
 synonym: "Liver failure" EXACT layperson []
 xref: SNOMEDCT_US:59927004
 xref: UMLS:C0085605
@@ -21074,6 +21076,7 @@ alt_id: HP:0004770
 alt_id: HP:0004781
 def: "Hair whose growth is slower than normal." [https://orcid.org/0000-0002-0736-9199]
 subset: hposlim_core
+synonym: "Poor hair growth" EXACT []
 synonym: "Slow growing hair" EXACT layperson []
 synonym: "Slow rate of hair growth" EXACT layperson [https://orcid.org/0000-0001-5889-4463]
 synonym: "Slow speed of hair growth" EXACT layperson [https://orcid.org/0000-0001-5889-4463]
@@ -21824,6 +21827,7 @@ id: HP:0002308
 name: Chiari malformation
 def: "Chiari malformation consists of a downward displacement of the cerebellar tonsils and the medulla through the foramen magnum, sometimes causing hydrocephalus as a result of obstruction of CSF outflow." [https://orcid.org/0000-0002-0736-9199, PMID:28613730]
 synonym: "Arnold-Chiari malformation" EXACT []
+synonym: "Cerebellar tonsillar ectopia" EXACT []
 xref: SNOMEDCT_US:253184003
 xref: UMLS:C0003803
 is_a: HP:0002438 ! Cerebellar malformation
@@ -39821,6 +39825,7 @@ id: HP:0004935
 name: Pulmonary artery atresia
 def: "A congenital anomaly with a narrowing or complete absence of the opening between the right ventricle and the pulmonary artery." [https://orcid.org/0000-0002-0736-9199]
 comment: Pulmonary artery atresia means that unoxygenated blood in the right ventricle can not be effectively pumped into the lung for oxygenation.
+synonym: "Atresia of the pulmonary artery" EXACT []
 synonym: "Pulmonary atresia" EXACT []
 xref: SNOMEDCT_US:10930001
 xref: SNOMEDCT_US:204443008
@@ -48772,6 +48777,7 @@ is_a: HP:0002795 ! Abnormal respiratory system physiology
 id: HP:0006538
 name: Recurrent bronchopulmonary infections
 def: "An increased susceptibility to bronchopulmonary infections as manifested by a history of recurrent bronchopulmonary infections." [https://orcid.org/0000-0002-0736-9199]
+synonym: "Recurrent bronchopneumonia" EXACT []
 synonym: "Recurrent infections in bronchi and lungs" BROAD layperson [https://orcid.org/0000-0001-5208-3432]
 xref: UMLS:C2169795
 is_a: HP:0002205 ! Recurrent respiratory infections
@@ -85032,6 +85038,7 @@ name: Recurrent sinusitis
 def: "A recurrent form of sinusitis." [https://orcid.org/0000-0002-0736-9199]
 comment: Recurring inflammation of the paranasal sinuses.
 synonym: "Recurrent sinus disease" RELATED layperson [https://orcid.org/0000-0001-5889-4463]
+synonym: "Recurrent sinus infections" EXACT []
 synonym: "Sinusitis, recurrent" EXACT [https://orcid.org/0000-0002-5316-1399]
 xref: SNOMEDCT_US:195788001
 xref: UMLS:C0581354
@@ -114409,6 +114416,7 @@ id: HP:0030053
 name: Stiff skin
 def: "An induration (hardening) of the skin" []
 synonym: "Indurated skin" EXACT []
+synonym: "Skin induration" EXACT []
 synonym: "Stiff skin" EXACT layperson []
 xref: UMLS:C3276815
 is_a: HP:0011121 ! Abnormal skin morphology
@@ -122959,7 +122967,7 @@ property_value: terms:creator https://orcid.org/0000-0002-0736-9199
 
 [Term]
 id: HP:0031134
-name: Cor triatrium sinister
+name: Cor triatriatum sinister
 def: "A developmental anomaly of the heart characterized by the presence of three atria because the left atrium is divided by an abnormal septum." [PMID:22379596]
 is_a: HP:0010774 ! Cor triatriatum
 property_value: dc:date "2017-06-10T13:02:05Z" xsd:dateTime
@@ -123880,6 +123888,7 @@ id: HP:0031244
 name: Swollen lip
 def: "Enlargement of the lip typically due to fluid buildup or inflammation." [https://orcid.org/0000-0001-5208-3432]
 synonym: "Edematous lip" EXACT []
+synonym: "Lip swelling" EXACT []
 synonym: "Swelling of the lip" EXACT []
 is_a: HP:0000159 ! Abnormal lip morphology
 property_value: dc:date "2017-08-12T13:02:05Z" xsd:dateTime
@@ -125149,6 +125158,9 @@ property_value: terms:creator https://orcid.org/0000-0002-0736-9199
 id: HP:0031389
 name: Abnormal MHC II surface expression
 def: "A deviation from the normal level of major histocompatibility complex class II molecules expressed at the cell surface." []
+comment: Human Leukocyte Antigen (HLA) is the human-specific name for the Major Histocompatibility Complex (MHC).
+synonym: "Abnormal human leukocyte antigen class II surface expression" EXACT []
+synonym: "Abnormal major histocompatibility complex class II surface expression" EXACT []
 is_a: HP:0010978 ! Abnormality of immune system physiology
 property_value: dc:date "2017-09-02T17:00:16Z" xsd:dateTime
 property_value: terms:creator https://orcid.org/0000-0002-0736-9199
@@ -125157,6 +125169,8 @@ property_value: terms:creator https://orcid.org/0000-0002-0736-9199
 id: HP:0031390
 name: Reduced MHC II surface expression
 def: "A reduction from the normal level of major histocompatibility complex class II molecules expressed at the cell surface." []
+synonym: "Abnormal HLA class II surface expression" EXACT []
+synonym: "Reduced human leukocyte antigen class II surface expression" EXACT []
 is_a: HP:0031389 ! Abnormal MHC II surface expression
 property_value: dc:date "2017-09-02T17:00:49Z" xsd:dateTime
 property_value: terms:creator https://orcid.org/0000-0002-0736-9199
@@ -177905,9 +177919,11 @@ property_value: terms:creator https://orcid.org/0000-0001-7941-2961
 id: HP:0500093
 name: Food allergy
 def: "Primary food allergies primarily occur as a result (most likely) of gastrointestinal sensitization to predominantly stable food allergens (glycoproteins). A secondary food allergy develops after primary sensitization to airborne allergens (e. g., pollen allergens) with subsequent reactions (due to cross-reactivity) to structurally related often labile allergens in (plant) foods." [PMID:27069254, PMID:27069841]
+synonym: "Allergic reaction to foods" EXACT []
 synonym: "Food allergy" EXACT layperson []
 synonym: "IgE-mediated food allergy" EXACT []
 synonym: "Immunoglobulin E-mediated food allergy" EXACT []
+synonym: "Reaction to food allergens" EXACT []
 is_a: HP:0012393 ! Allergy
 property_value: dc:date "2018-04-27T19:35:00Z" xsd:dateTime
 property_value: terms:creator https://orcid.org/0000-0001-7941-2961
@@ -189200,9 +189216,9 @@ id: HP:6000467
 name: Elevated urine D-lactate level
 def: "The amount of D-lactate in the urine, normalized for urine concentration, is above the upper limit of normal. L-lactate is a familiar molecule to the human body and is also produced in large amounts in human tissues, depending on metabolic conditions. In contrast, D-lactate is produced only in minute quantities in human tissues, and is therefore not detectable in the bloodstream under normal physiological conditions." [PMID:30931947]
 comment: Elevated urine D-lactate may be observed with D-lactic aciduria with susceptibility to gout.
-synonym: "https://github.com/obophenotype/human-phenotype-ontology/issues/8641" EXACT []
 is_a: HP:0012072 ! Aciduria
-property_value: IAO:0000233 https://orcid.org/0000-0002-0736-9199
+property_value: IAO:0000233 https://github.com/obophenotype/human-phenotype-ontology/issues/8641
+property_value: terms:contributor https://orcid.org/0000-0002-0736-9199
 
 [Term]
 id: HP:6000468
@@ -195144,6 +195160,99 @@ is_a: HP:0030839 ! Knee pain
 property_value: IAO:0000233 https://github.com/obophenotype/human-phenotype-ontology/issues/10745
 property_value: terms:contributor https://orcid.org/0000-0002-0736-9199
 
+[Term]
+id: HP:6001156
+name: Synovial crystals
+def: "The presence of microscopic crystalline structures in the synovial fluid (the lubricating fluid within joint cavities)." [PMID:21285711]
+comment: Synovial fluid analysis is a simple procedure requiring only a microscope fitted with polarized filters and a first-order red compensator. Synovial fluid is examined fresh without centrifugation, fixing or staining. Monosodium urate crystals responsible for gout and calcium pyrophosphate dehydrate crystals responsible for the related arthritis are of primary importance when performing a crystal search in synovial fluid in a clinical setting.
+synonym: "Bursa aspiration: crystals present" EXACT []
+synonym: "Crystals in synovial fluid" EXACT []
+is_a: HP:0025231 ! Abnormal synovial bursa morphology
+property_value: IAO:0000233 https://github.com/obophenotype/human-phenotype-ontology/issues/10820
+property_value: terms:contributor https://orcid.org/0000-0002-0736-9199
+
+[Term]
+id: HP:6001157
+name: Occupational exposure to frequent kneeling
+def: "A history of exposure to frequent squatting/kneeling and/or heavy lifting." [PMID:18597397]
+comment: Occupations that require frequent kneeling such as roofing, construction workers, plumbers, electricians, landscapers, gardeners, carpenters, and housekeepers may increase risk of prepatellar bursitis and knee osteoarthritis.
+synonym: "History of frequent kneeling" EXACT []
+is_a: HP:0035010 ! Occupational exposure history
+property_value: IAO:0000233 https://github.com/obophenotype/human-phenotype-ontology/issues/10823
+property_value: terms:contributor https://orcid.org/0000-0002-0736-9199
+
+[Term]
+id: HP:6001158
+name: Trochanteric pain
+def: "An unpleasant sensation characterized by physical discomfort (such as pricking, throbbing, or aching) localized to the structures around the greater trochanter (the bony prominence on the outer part of the femur)." []
+synonym: "Lateral hip pain" EXACT []
+synonym: "Pain at the lateral aspect of the hip" EXACT []
+synonym: "Pain on the outside of the hip" EXACT []
+is_a: HP:0030838 ! Hip pain
+property_value: IAO:0000233 https://github.com/obophenotype/human-phenotype-ontology/issues/10824
+property_value: terms:contributor https://orcid.org/0000-0002-0736-9199
+
+[Term]
+id: HP:6001159
+name: Pulsatile mass in extremity
+def: "A noticeable lump or swelling in the arm or leg that you can feel with you fingers and this lump is beating or pulsating, similar to the feeling of a heartbeat." []
+comment: This finding may be observed with conditions such as arteriovenous malformation located in the arm or leg or withulnar artery thrombosis.
+is_a: HP:0040064 ! Abnormality of limbs
+property_value: IAO:0000233 https://github.com/obophenotype/human-phenotype-ontology/issues/10832
+property_value: terms:contributor https://orcid.org/0000-0002-0736-9199
+
+[Term]
+id: HP:6001160
+name: Abnormal R wave
+def: "Any anomaly of the R wave of the EKG, which is the first upward deflection after the P wave. The R wave reflects early ventricular depolarisation." []
+is_a: HP:0003115 ! Abnormal EKG
+property_value: IAO:0000233 https://github.com/obophenotype/human-phenotype-ontology/issues/10839
+property_value: terms:contributor https://orcid.org/0000-0002-0736-9199
+
+[Term]
+id: HP:6001161
+name: Poor R-wave progression
+def: "Absence of the normal increase in size of the R wave in the precordial leads when advancing from lead V1 to V6 of the electrocardiogram." [PMID:35181482]
+comment: With normal R wave progression, the amplitude of the R wave gradually increased from V1 to V5 and decreases from V5 to V6. Abnormal R wave progression may be observed with myocardial infarction, cardiomyopathy, right or left ventricular hypertrophy, and other conditions.
+is_a: HP:6001160 ! Abnormal R wave
+property_value: IAO:0000233 https://github.com/obophenotype/human-phenotype-ontology/issues/10839
+property_value: terms:contributor https://orcid.org/0000-0002-0736-9199
+
+[Term]
+id: HP:6001162
+name: Prominent V1-V2 R wave
+def: "The R wave in leads V1-V2 is normally considerably smaller in amplitude than the S wave in the same leads. Prominent R wave in these leads implies the R wave is larger than the S-wave, which may indicate cardiovascular pathology. This term includes Tall R wave in lead V1, which is defined by a R/S ratio greater than 1." [PMID:11593472]
+comment: This electrocardiographic finding exists as a normal variant in only 1% of patients. Physicians should therefore be familiar with the differential diagnosis for this important QRS configuration. The electrocardiographic entities which can present with this finding include right bundle branch block, left ventricular ectopy, right ventricular hypertrophy, acute right ventricular dilation (acute right heart strain), type a Wolff-Parkinson-White syndrome, posterior myocardial infarction, hypertrophic cardiomyopathy, progressive muscular dystrophy, dextrocardia, misplaced precordial leads, and normal variant.
+synonym: "High voltage R wave in V1/V2" EXACT []
+synonym: "Prominent R wave in lead V1" EXACT []
+is_a: HP:6001160 ! Abnormal R wave
+property_value: IAO:0000233 https://github.com/obophenotype/human-phenotype-ontology/issues/10839
+property_value: terms:contributor https://orcid.org/0000-0002-0736-9199
+
+[Term]
+id: HP:6001163
+name: Finger mass
+def: "An abnormal enlargement or swelling localized to a finger." []
+comment: The word mass is usually used at an early stage of the diagnostic workup before the precise nature of the swelling has been determined.
+synonym: "Bump on finger" EXACT []
+synonym: "Finger growth" EXACT []
+synonym: "Lump on finger" EXACT []
+is_a: HP:0001167 ! Abnormal finger morphology
+property_value: IAO:0000233 https://github.com/obophenotype/human-phenotype-ontology/issues/10842
+property_value: terms:contributor https://orcid.org/0000-0002-0736-9199
+
+[Term]
+id: HP:6001164
+name: Foot mass
+def: "An abnormal enlargement or swelling localized to a foot." []
+comment: The word mass is usually used at an early stage of the diagnostic workup before the precise nature of the swelling has been determined.
+synonym: "Bump on foot" EXACT []
+synonym: "Foot growth" EXACT []
+synonym: "Lump on foot" EXACT []
+is_a: HP:0001760 ! Abnormal foot morphology
+property_value: IAO:0000233 https://github.com/obophenotype/human-phenotype-ontology/issues/10844
+property_value: terms:contributor https://orcid.org/0000-0002-0736-9199
+
 [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/2024-12-12/patterns/definitions.owl>
-Annotation(owl:versionInfo "2024-12-12")
+<http://purl.obolibrary.org/obo/hp/releases/2025-01-16/patterns/definitions.owl>
+Annotation(owl:versionInfo "2025-01-16")