The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species.

In biology and biomedicine, relating phenotypic outcomes with genetic variation and environmental factors remains a challenge: patient phenotypes may not match known diseases, candidate variants may be in genes that haven\u27t been characterized, research organisms may not recapitulate human or veterinary diseases, environmental factors affecting disease outcomes are unknown or undocumented, and many resources must be queried to find potentially significant phenotypic associations. The Monarch Initiative (https://monarchinitiative.org) integrates information on genes, variants, genotypes, phenotypes and diseases in a variety of species, and allows powerful ontology-based search. We develop many widely adopted ontologies that together enable sophisticated computational analysis, mechanistic discovery and diagnostics of Mendelian diseases. Our algorithms and tools are widely used to identify animal models of human disease through phenotypic similarity, for differential diagnostics and to facilitate translational research. Launched in 2015, Monarch has grown with regards to data (new organisms, more sources, better modeling); new API and standards; ontologies (new Mondo unified disease ontology, improvements to ontologies such as HPO and uPheno); user interface (a redesigned website); and community development. Monarch data, algorithms and tools are being used and extended by resources such as GA4GH and NCATS Translator, among others, to aid mechanistic discovery and diagnostics

The Human Phenotype Ontology in 2024: phenotypes around the world.

The Human Phenotype Ontology (HPO) is a widely used resource that comprehensively organizes and defines the phenotypic features of human disease, enabling computational inference and supporting genomic and phenotypic analyses through semantic similarity and machine learning algorithms. The HPO has widespread applications in clinical diagnostics and translational research, including genomic diagnostics, gene-disease discovery, and cohort analytics. In recent years, groups around the world have developed translations of the HPO from English to other languages, and the HPO browser has been internationalized, allowing users to view HPO term labels and in many cases synonyms and definitions in ten languages in addition to English. Since our last report, a total of 2239 new HPO terms and 49235 new HPO annotations were developed, many in collaboration with external groups in the fields of psychiatry, arthrogryposis, immunology and cardiology. The Medical Action Ontology (MAxO) is a new effort to model treatments and other measures taken for clinical management. Finally, the HPO consortium is contributing to efforts to integrate the HPO and the GA4GH Phenopacket Schema into electronic health records (EHRs) with the goal of more standardized and computable integration of rare disease data in EHRs

OpenVIVO: Transparency in Scholarship

OpenVIVO is a free and open-hosted semantic web platform that anyone can join and that gathers and shares open data about scholarship in the world. OpenVIVO, based on the VIVO open-source platform, provides transparent access to data about the scholarly work of its participants. OpenVIVO demonstrates the use of persistent identifiers, the automatic real-time ingest of scholarly ecosystem metadata, the use of VIVO-ISF and related ontologies, the attribution of work, and the publication and reuse of data—all critical components of presenting, preserving, and tracking scholarship. The system was created by a cross-institutional team over the course of 3 months. The team created and used RDF models for research organizations in the world based on Digital Science GRID data, for academic journals based on data from CrossRef and the US National Library of Medicine, and created a new model for attribution of scholarly work. All models, data, and software are available in open repositories

monarch-initiative/mondo: v2023-09-12

Overview: Number of new terms: 379 Number of changed labels: 28 Number of changed definitions: 508 Number obsoleted terms: 6 Number of new obsoletion candidates: 236 Number of terms who were previously candidate for obsoletion and are now not anymore: 1 New terms Mondo ID Label Definition MONDO:0100524 ASAH1-related sphingolipidosis A spectrum of disorders that includes Farber disease and spinal muscular atrophy with progressive myoclonic epilepsy. Both disorders are caused by mutations in the ASAH1 gene that encodes the lysosomal hydrolase that breaks down the bioactive lipid, ceramide. MONDO:0100525 TCF7L2-related neurodevelopmental disorder A newly discovered disorder caused by a change (variant or mutation) in the TCF7L2 gene. This mutation may be responsible for developmental delays in childhood, intellectual disability, autism, myopia, ADHD, abnormal physical features and other problems. There is a wide spectrum of severity for individuals affected with TRND. Many of the symptoms of TRND overlap with other neurodevelopmental disorders. TRND must be diagnosed with a genetic test and cannot be diagnosed by symptoms alone. MONDO:0100526 breast-ovarian cancer, familial, susceptibility to MONDO:0100527 dysplastic cortical hyperostosis, Kozlowski-Tsuruta type An extremely rare primary bone dysplasia with increased bone density characterized by lethal neonatal dwarfism with hydrops, narrow chest and short limbs with extensive cortical thickening of all long bones, ribs, clavicles and scapulae, and coronal clefts in vertebral bodies. MONDO:0100528 Hao-Fountain syndrome due to 16p13.2 microdeletion A partial deletion of the short arm of chromosome 16 characterized by developmental delay, intellectual disability, speech delay, autism spectrum disorder, epilepsy, hypogonadism, and hypotonia. The behavioral profile includes impulsivity, compulsivity, stubbornness, manipulative behaviors, temper tantrums, and aggressive behaviors. MONDO:0800448 leukoencephalopathy with vanishing white matter A new leukoencephalopathy, the CACH syndrome (Childhood Ataxia with Central nervous system Hypomyelination) or VWM (Vanishing White Matter) was identified on clinical and MRI criteria. Classically, this disease is characterized by (1) an onset between 2 and 5 years of age, with a cerebello-spastic syndrome exacerbated by episodes of fever or head trauma leading to death after 5 to 10 years of disease evolution, (2) a diffuse involvement of the white matter on cerebral MRI with a CSF-like signal intensity (cavitation), (3) a recessive autosomal mode of inheritance, (4) neuropathologic findings consistent with a cavitating orthochromatic leukodystrophy with increased number of oligodendrocytes with sometimes \foamy'' aspect." MONDO:0957202 spermatogenic failure, X-linked, 7 MONDO:0957203 intellectual developmental disorder, X-linked 111 MONDO:0957204 autoinflammation with pulmonary and cutaneous vasculitis MONDO:0957208 pituitary hormone deficiency, combined or isolated, 8 MONDO:0957210 neurooculorenal syndrome MONDO:0957211 neurodegeneration and seizures due to copper transport defect MONDO:0957215 congenital myopathy 20 MONDO:0957216 premature ovarian failure 21 MONDO:0957217 cortical dysplasia, complex, with other brain malformations 12 MONDO:0957218 neurodevelopmental disorder with microcephaly and speech delay, with or without brain abnormalities MONDO:0957220 oocyte/zygote/embryo maturation arrest 17 MONDO:0957221 spastic paraplegia 70, autosomal recessive MONDO:0957224 congenital myopathy 21 with early respiratory failure MONDO:0957225 neurodegeneration with developmental delay, early respiratory failure, myoclonic seizures, and brain abnormalities MONDO:0957228 intellectual developmental disorder, autosomal dominant 71, with behavioral abnormalities MONDO:0957229 hatipoglu immunodeficiency syndrome MONDO:0957230 oocyte/zygote/embryo maturation arrest 18 MONDO:0957231 oocyte/zygote/embryo maturation arrest 19 MONDO:0957240 cone-rod dystrophy 24 MONDO:0957247 congenital myopathy 22A, classic MONDO:0957248 developmental and epileptic encephalopathy 31B MONDO:0957249 spermatogenic failure 82 MONDO:0957250 spermatogenic failure 83 MONDO:0957252 ciliary dyskinesia, primary, 50 MONDO:0957253 diarrhea 13 MONDO:0957254 mitochondrial complex V (ATP synthase) deficiency, nuclear type 4A MONDO:0957255 mitochondrial complex V (ATP synthase) deficiency, nuclear type 7 MONDO:0957260 combined low LDL and fibrinogen MONDO:0957261 pulmonary fibrosis and/or bone marrow failure syndrome, telomere-related, 7 MONDO:0957262 osteopetrosis, autosomal recessive 9 MONDO:0957263 pulmonary fibrosis and/or bone marrow failure syndrome, telomere-related, 8 MONDO:0957264 cerebroretinal microangiopathy with calcifications and cysts 3 MONDO:0957265 congenital myopathy 22B, severe fetal MONDO:0957266 RECON progeroid syndrome MONDO:0957267 neurodevelopmental disorder with intracranial hemorrhage, seizures, and spasticity MONDO:0957268 hypersulfaturia MONDO:0957270 muscular dystrophy, limb-girdle, autosomal recessive 28 MONDO:0957271 autoinflammatory disease, systemic, with vasculitis MONDO:0957273 Charcot-Marie-Tooth disease, dominant intermediate A MONDO:0957274 spastic paraplegia 89, autosomal recessive MONDO:0957278 oocyte/zygote/embryo maturation arrest 20 MONDO:0957279 auditory neuropathy, autosomal dominant 2 MONDO:0957281 nemaline myopathy 5B, autosomal recessive, childhood-onset MONDO:0957284 nemaline myopathy 5C, autosomal dominant MONDO:0957288 intellectual developmental disorder, autosomal recessive 79 MONDO:0957294 pulmonary fibrosis and/or bone marrow failure syndrome, telomere-related, 9 MONDO:0957301 spermatogenic failure 84 MONDO:0957303 palmoplantar keratoderma, epidermolytic, 2 MONDO:0957307 woolly hair-skin fragility syndrome MONDO:0957308 spastic paraplegia 90A, autosomal dominant MONDO:0957309 spastic paraplegia 90B, autosomal recessive MONDO:0957314 retinitis pigmentosa 97 MONDO:0957337 isolated chorioretinal dystrophy MONDO:0957341 secondary early-onset glaucoma MONDO:0957382 multiple mitochondrial dysfunctions syndrome 7 MONDO:0957385 dystonia 37, early-onset, with striatal lesions MONDO:0957386 neurodevelopmental disorder with motor and language delay, ocular defects, and brain abnormalities MONDO:0957388 autoimmune disease, multisystem, infantile-onset, 3 MONDO:0957396 ciliary dyskinesia, primary, 51 MONDO:0957397 intellectual developmental disorder, autosomal dominant 72 MONDO:0957403 periodic fever syndrome of childhood MONDO:0957404 pyogenic autoinflammatory syndrome of childhood MONDO:0957405 granulomatous autoinflammatory syndrome of childhood MONDO:0957408 type 1 interferonopathy of childhood MONDO:0957421 borna virus encephalitis MONDO:0957423 immunotherapy induced hypophysitis MONDO:0957426 autosomal recessive hyper-IgE syndrome MONDO:0957427 B-lymphoblastic leukemia/lymphoma with t(7;9)(q11.2;p13.2) MONDO:0957428 B-lymphoblastic leukemia/lymphoma with t(17;19) MONDO:0957430 childhood-onset schizophrenia MONDO:0957431 endogenous Cushing syndrome MONDO:0957432 neonatal compartment syndrome MONDO:0957433 primary pulmonary vein stenosis MONDO:0957442 autosomal recessive ataxia due to PEX16 deficiency MONDO:0957443 autosomal recessive ataxia due to PEX2 deficiency MONDO:0957451 non-terminal myelocystocele A rare closed spinal dysraphism characterized by myelocystocele located above the conus region. Also considered as a form of saccular limited dorsal myeloschisis. MONDO:0957452 segmental arterial mediolysis MONDO:0957453 true myelomeningocele A rare open neural tube defect characterized by no other malformation than myelomeningocele (spina bifida with a neural placode exposed at the top of a non-epidermised dysplasic meninges sac and Chiari II malformation). MONDO:0957454 hemi-myelomeningocele A very rare form of composite dysraphism characterized by the presence of a split cord malformation and a myelomeningocele on one of the two hemicords. Hemicords can be in a single dural sac or in two separated dural sacs. Other spinal cord malformations can be associated. Due to the comparable prognosis it is considered as a subtype of myelomeningocele. MONDO:0957456 classical dermatomyositis MONDO:0957458 adermatopathic dermatomyositis MONDO:0957459 congenital esophageal stenosis MONDO:0957460 spontaneous intestinal perforation MONDO:0957461 primary tuberculous lymphadenitis MONDO:0957462 primary pulmonary tuberculosis MONDO:0957463 primary bone and joint tuberculosis MONDO:0957464 primary cutaneous tuberculosis MONDO:0957465 multifocal tuberculosis MONDO:0957466 primary tuberculosis of the digestive system MONDO:0957467 primary genito-urinary tuberculosis MONDO:0957473 craniosynostosis-facial dysmorphism-chiari-1 malformation-developmental and language delay syndrome MONDO:0957476 isolated persistent urogenital sinus MONDO:0957477 MYT1L-related developmental delay-intellectual disability-obesity syndrome MONDO:0957481 idiopathic pregnancy-associated osteoporosis MONDO:0957487 idiopathic catatonia MONDO:0957494 autoinflammatory disease, multisystem, with immune dysregulation, X-linked MONDO:0957495 hemolytic uremic syndrome, atypical, 8, with rhizomelic short stature MONDO:0957496 intellectual developmental disorder, X-linked 112 MONDO:0957497 disabling pansclerotic morphea of childhood MONDO:0957530 breast-ovarian cancer, familial, susceptibility to, 5 MONDO:0957531 neurodevelopmental disorder with microcephaly and movement abnormalities MONDO:0957533 megalencephalic leukoencephalopathy with subcortical cysts 3 MONDO:0957534 megalencephalic leukoencephalopathy with subcortical cysts 4, remitting MONDO:0957535 immunodeficiency 112 MONDO:0957536 intellectual developmental disorder, autosomal dominant 73 MONDO:0957537 combined oxidative phosphorylation deficiency 58 MONDO:0957538 amyotrophic lateral sclerosis 28 MONDO:0957539 dystonia 22, juvenile-onset MONDO:0957540 congenital disorder of glycosylation, type IIaa MONDO:0957541 neurodevelopmental disorder with hypotonia and speech delay, with or without seizures MONDO:0957542 dystonia 22, adult-onset MONDO:0957543 auriculocondylar syndrome 4 MONDO:0957544 auriculocondylar syndrome 2B MONDO:0957545 cardiomyopathy, dilated, 2I MONDO:0957556 congenital pulmonary vein atresia MONDO:1010001 epilepsy, non-human animal Epilepsy that occurs in non-human animals. MONDO:1010002 myoclonus, non-human animal Myoclonus that occurs in non-human animals. MONDO:1010003 narcolepsy, non-human animal Narcolepsy that occurs in non-human animals. MONDO:1010004 paroxysmal dyskinesia, non-human animal Paroxysmal dyskinesia that occurs in non-human animals. MONDO:1010005 autism spectrum disorder, non-human animal Autism spectrum disorder that occurs in non-human animals. MONDO:1010006 Phelan-McDermid syndrome, non-human animal Phelan-McDermid syndrome that occurs in non-human animals. MONDO:1010007 subvalvular aortic stenosis, non-human animal Subvalvular aortic stenosis that occurs in non-human animals. MONDO:1010008 atherosclerosis, non-human animal Atherosclerosis that occurs in non-human animals. MONDO:1010009 atrial septal defect, non-human animal Atrial septal defect that occurs in non-human animals. MONDO:1010010 cardiomyopathy, non-human animal Cardiomyopathy that occurs in non-human animals. MONDO:1010011 dilated cardiomyopathy, non-human animal Dilated cardiomyopathy that occurs in non-human animals. MONDO:1010012 conotruncal heart malformations, non-human animal Conotruncal heart malformations that occurs in non-human animals. MONDO:1010013 cor triatriatum dexter, non-human animal Cor triatriatum dexter that occurs in non-human animals. MONDO:1010014 essential hypertension, non-human animal Essential hypertension that occurs in non-human animals. MONDO:1010015 hypertrophic cardiomyopathy, non-human animal Hypertrophic cardiomyopathy that occurs in non-human animals. MONDO:1010016 mitral valve stenosis, non-human animal Mitral valve stenosis that occurs in non-human animals. MONDO:1010017 patent ductus arteriosus, non-human animal Patent ductus arteriosus that occurs in non-human animals. MONDO:1010018 persistent truncus arteriosus, non-human animal Persistent truncus arteriosus that occurs in non-human animals. MONDO:1010019 arrhythmogenic right ventricular cardiomyopathy, non-human animal Arrhythmogenic right ventricular cardiomyopathy that occurs in non-human animals. MONDO:1010020 supravalvular aortic stenosis, non-human animal Supravalvular aortic stenosis that occurs in non-human animals. MONDO:1010021 tetralogy of fallot, non-human animal Tetralogy of fallot that occurs in non-human animals. MONDO:1010022 ventricular septal defect, non-human animal Ventricular septal defect that occurs in non-human animals. MONDO:1010023 patent ductus venosus, non-human animal Patent ductus venosus that occurs in non-human animals. MONDO:1010024 atrial fibrillation, non-human animal Atrial fibrillation that occurs in non-human animals. MONDO:1010025 Wolff-Parkinson-White syndrome, non-human animal Wolff-Parkinson-White syndrome that occurs in non-human animals. MONDO:1010026 Budd-Chiari syndrome, non-human animal Budd-Chiari syndrome that occurs in non-human animals. MONDO:1010027 endocardial fibroelastosis, non-human animal Endocardial fibroelastosis that occurs in non-human animals. MONDO:1010028 cerebral amyloid angiopathy, non-human animal Cerebral amyloid angiopathy that occurs in non-human animals. MONDO:1010031 triploidy, non-human animal Triploidy that occurs in non-human animals. MONDO:1010032 Jacobsen syndrome, non-human animal Jacobsen syndrome that occurs in non-human animals. MONDO:1010033 holoprosencephaly, non-human animal Holoprosencephaly that occurs in non-human animals. MONDO:1010034 cleft lip with or without cleft palate, non-human animal Cleft lip with or without cleft palate that occurs in non-human animals. MONDO:1010035 mandibulofacial dysostosis, non-human animal Mandibulofacial dysostosis that occurs in non-human animals. MONDO:1010036 frontonasal dysplasia, non-human animal Frontonasal dysplasia that occurs in non-human animals. MONDO:1010037 cleft palate, non-human animal Cleft palate that occurs in non-human animals. MONDO:1010038 gingival hypertrophy, non-human animal Gingival hypertrophy that occurs in non-human animals. MONDO:1010039 megacolon, non-human animal Megacolon that occurs in non-human animals. MONDO:1010040 pyloric stenosis, non-human animal Pyloric stenosis that occurs in non-human animals. MONDO:1010041 Meckel diverticulum, non-human animal Meckel diverticulum that occurs in non-human animals. MONDO:1010042 protein-losing enteropathy, non-human animal Protein-losing enteropathy that occurs in non-human animals. MONDO:1010043 cystic fibrosis, non-human animal Cystic fibrosis that occurs in non-human animals. MONDO:1010044 microvillus inclusion disease, non-human animal Microvillus inclusion disease that occurs in non-human animals. MONDO:1010045 diprosopus, non-human animal Diprosopus that occurs in non-human animals. MONDO:1010046 patent urachus, non-human animal Patent urachus that occurs in non-human animals. MONDO:1010047 spina bifida, non-human animal Spina bifida that occurs in non-human animals. MONDO:1010048 spina bifida occulta, non-human animal Spina bifida occulta that occurs in non-human animals. MONDO:1010049 acromegaly, non-human animal Acromegaly that occurs in non-human animals. MONDO:1010050 congenital adrenal hyperplasia, non-human animal Congenital adrenal hyperplasia that occurs in non-human animals. MONDO:1010051 diabetes insipidus, non-human animal Diabetes insipidus that occurs in non-human animals. MONDO:1010052 diabetes mellitus, non-human animal Diabetes mellitus that occurs in non-human animals. MONDO:1010053 familial goiter, non-human animal Familial goiter that occurs in non-human animals. MONDO:1010054 hyperparathyroidism, non-human animal Hyperparathyroidism that occurs in non-human animals. MONDO:1010055 hyperthyroidism, non-human animal Hyperthyroidism that occurs in non-human animals. MONDO:1010056 hypoparathyroidism, non-human animal Hypoparathyroidism that occurs in non-human animals. MONDO:1010057 congenital hypothyroidism, non-human animal Congenital hypothyroidism that occurs in non-human animals. MONDO:1010058 exocrine pancreatic insufficiency, non-human animal Exocrine pancreatic insufficiency that occurs in non-human animals. MONDO:1010059 thyroiditis, non-human animal Thyroiditis that occurs in non-human animals. MONDO:1010060 pheochromocytoma, non-human animal Pheochromocytoma that occurs in non-human animals. MONDO:1010061 hyperaldosteronism, non-human animal Hyperaldosteronism that occurs in non-human animals. MONDO:1010062 congenital adrenal hyperplasia due to 11-beta hydroxylase deficiency, non-human animal Congenital adrenal hyperplasia due to 11-beta hydroxylase deficiency that occurs in non-human animals. MONDO:1010063 congenital adrenal hypoplasia, non-human animal Congenital adrenal hypoplasia that occurs in non-human animals. MONDO:1010066 microcephaly, non-human animal Microcephaly that occurs in non-human animals. MONDO:1010067 omphalocele, non-human animal Omphalocele that occurs in non-human animals. MONDO:1010068 situs inversus, non-human animal Situs inversus that occurs in non-human animals. MONDO:1010069 autoimmune thrombocytopenia, non-human animal Autoimmune thrombocytopenia that occurs in non-human animals. MONDO:1010070 Chediak-Higashi syndrome, non-human animal Chediak-Higashi syndrome that occurs in non-human animals. MONDO:1010071 factor VII deficiency, non-human animal Factor VII deficiency that occurs in non-human animals. MONDO:1010072 factor X deficiency, non-human animal Factor X deficiency that occurs in non-human animals. MONDO:1010073 factor XI deficiency, non-human animal Factor XI deficiency that occurs in non-human animals. MONDO:1010074 factor XII deficiency, non-human animal Factor XII deficiency that occurs in non-human animals. MONDO:1010075 hemophilia B, non-human animal Hemophilia B that occurs in non-human animals. MONDO:1010076 hypereosinophilic syndrome, non-human animal Hypereosinophilic syndrome that occurs in non-human animals. MONDO:1010077 Pelger-Huet anomaly, non-human animal Pelger-Huet anomaly that occurs in non-human animals. MONDO:1010078 polycythemia, non-human animal Polycythemia that occurs in non-human animals. MONDO:1010079 prekallikrein deficiency, non-human animal Prekallikrein deficiency that occurs in non-human animals. MONDO:1010080 thrombocytopenia, non-human animal Thrombocytopenia that occurs in non-human animals. MONDO:1010081 autoimmune thrombocytopenic purpura, non-human animal Autoimmune thrombocytopenic purpura that occurs in non-human animals. MONDO:1010082 Evans syndrome, non-human animal Evans syndrome that occurs in non-human animals. MONDO:1010083 Scott Syndrome, non-human animal Scott Syndrome that occurs in non-human animals. MONDO:1010085 factor XIII deficiency, non-human animal Factor XIII deficiency that occurs in non-human animals. MONDO:1010086 myeloperoxidase deficiency, non-human animal Myeloperoxidase deficiency that occurs in non-human animals. MONDO:1010090 anotia, non-human animal Anotia that occurs in non-human animals. MONDO:1010091 microtia, non-human animal Microtia that occurs in non-human animals. MONDO:1010092 AA amyloidosis, non-human animal AA amyloidosis that occurs in non-human animals. MONDO:1010093 AL amyloidosis, non-human animal AL amyloidosis that occurs in non-human animals. MONDO:1010094 analphalipoproteinaemia, non-human animal Analphalipoproteinaemia that occurs in non-human animals. MONDO:1010095 citrullinemia, non-human animal Citrullinemia that occurs in non-human animals. MONDO:1010099 pyruvate kinase deficiency of erythrocyte, non-human animal Pyruvate kinase deficiency of erythrocyte that occurs in non-human animals. MONDO:1010101 galactosemia, non-human animal Galactosemia that occurs in non-human animals. MONDO:1010102 porphyria cutanea tarda, non-human animal Porphyria cutanea tarda that occurs in non-human animals. MONDO:1010103 eclampsia, non-human animal Eclampsia that occurs in non-human animals. MONDO:1010104 trimethylaminuria (fishy taint), non-human animal Trimethylaminuria (fishy taint) that occurs in non-human animals. MONDO:1010105 pyruvate dehydrogenase deficiency, non-human animal Pyruvate dehydrogenase deficiency that occurs in non-human animals. MONDO:1010106 multiple acyl-coa dehydrogenase deficiency, non-human animal Multiple acyl-coa dehydrogenase deficiency that occurs in non-human animals. MONDO:1010107 acute intermittent porphyria, non-human animal Acute intermittent porphyria that occurs in non-human animals. MONDO:1010109 dihydropyrimidinase deficiency, non-human animal Dihydropyrimidinase deficiency that occurs in non-human animals. MONDO:1010110 hyperphosphatemia, non-human animal Hyperphosphatemia that occurs in non-human animals. MONDO:1010113 glucocorticoid resistance, non-human animal Glucocorticoid resistance that occurs in non-human animals. MONDO:1010114 phenylketonuria, non-human animal Phenylketonuria that occurs in non-human animals. MONDO:1010115 c8 deficiency, non-human animal C8 deficiency that occurs in non-human animals. MONDO:10

OpenVIVO: A VIVO anyone can join

Poster presented June 14, 2016 at OR2016, Dublin I

The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species

In biology and biomedicine, relating phenotypic outcomes with genetic variation and environmental factors remains a challenge: patient phenotypes may not match known diseases, candidate variants may be in genes that haven't been characterized, research organisms may not recapitulate human or veterinary diseases, environmental factors affecting disease outcomes are unknown or undocumented, and many resources must be queried to find potentially significant phenotypic associations. The Monarch Initiative (https://monarchinitiative.org) integrates information on genes, variants, genotypes, phenotypes and diseases in a variety of species, and allows powerful ontology-based search. We develop many widely adopted ontologies that together enable sophisticated computational analysis, mechanistic discovery and diagnostics of Mendelian diseases. Our algorithms and tools are widely used to identify animal models of human disease through phenotypic similarity, for differential diagnostics and to facilitate translational research. Launched in 2015, Monarch has grown with regards to data (new organisms, more sources, better modeling); new API and standards; ontologies (new Mondo unified disease ontology, improvements to ontologies such as HPO and uPheno); user interface (a redesigned website); and community development. Monarch data, algorithms and tools are being used and extended by resources such as GA4GH and NCATS Translator, among others, to aid mechanistic discovery and diagnostics

The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species.

In biology and biomedicine, relating phenotypic outcomes with genetic variation and environmental factors remains a challenge: patient phenotypes may not match known diseases, candidate variants may be in genes that haven't been characterized, research organisms may not recapitulate human or veterinary diseases, environmental factors affecting disease outcomes are unknown or undocumented, and many resources must be queried to find potentially significant phenotypic associations. The Monarch Initiative (https://monarchinitiative.org) integrates information on genes, variants, genotypes, phenotypes and diseases in a variety of species, and allows powerful ontology-based search. We develop many widely adopted ontologies that together enable sophisticated computational analysis, mechanistic discovery and diagnostics of Mendelian diseases. Our algorithms and tools are widely used to identify animal models of human disease through phenotypic similarity, for differential diagnostics and to facilitate translational research. Launched in 2015, Monarch has grown with regards to data (new organisms, more sources, better modeling); new API and standards; ontologies (new Mondo unified disease ontology, improvements to ontologies such as HPO and uPheno); user interface (a redesigned website); and community development. Monarch data, algorithms and tools are being used and extended by resources such as GA4GH and NCATS Translator, among others, to aid mechanistic discovery and diagnostics

The Human Phenotype Ontology in 2024: phenotypes around the world.

The Human Phenotype Ontology (HPO) is a widely used resource that comprehensively organizes and defines the phenotypic features of human disease, enabling computational inference and supporting genomic and phenotypic analyses through semantic similarity and machine learning algorithms. The HPO has widespread applications in clinical diagnostics and translational research, including genomic diagnostics, gene-disease discovery, and cohort analytics. In recent years, groups around the world have developed translations of the HPO from English to other languages, and the HPO browser has been internationalized, allowing users to view HPO term labels and in many cases synonyms and definitions in ten languages in addition to English. Since our last report, a total of 2239 new HPO terms and 49235 new HPO annotations were developed, many in collaboration with external groups in the fields of psychiatry, arthrogryposis, immunology and cardiology. The Medical Action Ontology (MAxO) is a new effort to model treatments and other measures taken for clinical management. Finally, the HPO consortium is contributing to efforts to integrate the HPO and the GA4GH Phenopacket Schema into electronic health records (EHRs) with the goal of more standardized and computable integration of rare disease data in EHRs