HP

HPO
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:43.873620

metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

hpo
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:43.873620

Other names: HP, HPO, hpo

The Human Phenotype Ontology (HPO) provides a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as Atrial septal defect. The HPO is currently being developed using the medical literature, Orphanet, DECIPHER, and OMIM.

Webpage:

https://hpo.jax.org/

Licence:

Name: HPO - specific
URL: https://hpo.jax.org/app/license

Publications: (7)

Publications
More detailed information about this field from each metasource.

The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease
PMID: 18950739
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

metasource: Fairsharing.org
version: FAIRsharing.org: HP; Human Phenotype Ontology; DOI: https://doi.org/10.25504/FAIRsharing.kbtt7f; Last edited: July 9, 2019, 10:37 a.m.; Last accessed: Jan 03 2022 7:12 p.m.

The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data
PMID: 24217912
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

metasource: Fairsharing.org
version: FAIRsharing.org: HP; Human Phenotype Ontology; DOI: https://doi.org/10.25504/FAIRsharing.kbtt7f; Last edited: July 9, 2019, 10:37 a.m.; Last accessed: Jan 03 2022 7:12 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:43.873620

The Human Phenotype Ontology in 2017
PMID: 27899602
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

metasource: Fairsharing.org
version: FAIRsharing.org: HP; Human Phenotype Ontology; DOI: https://doi.org/10.25504/FAIRsharing.kbtt7f; Last edited: July 9, 2019, 10:37 a.m.; Last accessed: Jan 03 2022 7:12 p.m.

Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources
PMID: 30476213
metasource: Fairsharing.org
version: FAIRsharing.org: HP; Human Phenotype Ontology; DOI: https://doi.org/10.25504/FAIRsharing.kbtt7f; Last edited: July 9, 2019, 10:37 a.m.; Last accessed: Jan 03 2022 7:12 p.m.

The human phenotype ontology
PMID: 20412080
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

metasource: Fairsharing.org
version: FAIRsharing.org: HP; Human Phenotype Ontology; DOI: https://doi.org/10.25504/FAIRsharing.kbtt7f; Last edited: July 9, 2019, 10:37 a.m.; Last accessed: Jan 03 2022 7:12 p.m.

http://human-phenotype-ontology.github.io/license.html
metasource: Biontology / Bioportal
version: hp/releases/2022-10-05 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/HP

http://dx.doi.org/10.1093/nar/gkaa1043
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease PubMed citations: 371.

371 articles citing: The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease

Etiologic Classification of Diffuse Parenchymal (Interstitial) Lung Diseases. PMID:35330072
Validation of a computational phenotype for finding patients eligible for genetic testing for pathogenic PTEN variants across three centers. PMID:35321655
Enhancer promoter interactome and Mendelian randomization identify network of druggable vascular genes in coronary artery disease. PMID:35246263
Whole genome sequencing for the diagnosis of neurological repeat expansion disorders in the UK: a retrospective diagnostic accuracy and prospective clinical validation study. PMID:35182509
Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases. PMID:35134823
Prioritization of putatively detrimental variants in euploid miscarriages. PMID:35132093
Cardiovascular Phenotypes Profiling for L-Transposition of the Great Arteries and Prognosis Analysis. PMID:35127856
Clin.iobio: A Collaborative Diagnostic Workflow to Enable Team-Based Precision Genomics. PMID:35055388
Mitochondrial disease manifestations in relation to transcriptome location and function. PMID:34972656
Identifying essential genes across eukaryotes by machine learning. PMID:34859210
Quantitative dissection of multilocus pathogenic variation in an Egyptian infant with severe neurodevelopmental disorder resulting from multiple molecular diagnoses. PMID:34816580
The Immune Deficiency and Dysregulation Activity (IDDA2.1 'Kaleidoscope') Score and Other Clinical Measures in Inborn Errors of Immunity. PMID:34797428
Refining the Diagnosis of Growth-Related Muscle Abnormalities in Chickens Based on the Nomenclature Used to Characterise Human Myopathies. PMID:34790133
Epigenetic modelling of former, current and never smokers. PMID:34789321
A Visual Phenotype-Based Differential Diagnosis Process for Rare Diseases. PMID:34751921
Biomedical Ontologies to Guide AI Development in Radiology. PMID:34724143
KGDAL: Knowledge Graph Guided Double Attention LSTM for Rolling Mortality Prediction for AKI-D Patients. PMID:34541583
Generalized and social anxiety disorder interactomes show distinctive overlaps with striosome and matrix interactomes. PMID:34526518
Deep clinicopathological phenotyping identifies a previously unrecognized pathogenic EMD splice variant. PMID:34524739
Pleiotropy data resource as a primer for investigating co-morbidities/multi-morbidities and their role in disease. PMID:34524473
Establishing the phenotypic spectrum of ZTTK syndrome by analysis of 52 individuals with variants in SON. PMID:34521999
Evaluating, Filtering and Clustering Genetic Disease Cohorts Based on Human Phenotype Ontology Data with Cohort Analyzer. PMID:34442375
DNA Methylation Alterations in Blood Cells of Toddlers with Down Syndrome. PMID:34440289
Linking common human diseases to their phenotypes; development of a resource for human phenomics. PMID:34425897
X-CNV: genome-wide prediction of the pathogenicity of copy number variations. PMID:34407882
FLAME: A Web Tool for Functional and Literature Enrichment Analysis of Multiple Gene Lists. PMID:34356520
Text mining of gene-phenotype associations reveals new phenotypic profiles of autism-associated genes. PMID:34315992
Prioritizing and characterizing functionally relevant genes across human tissues. PMID:34270548
Strategies to Uplift Novel Mendelian Gene Discovery for Improved Clinical Outcomes. PMID:34220947
Identifying Key Somatic Copy Number Alterations Driving Dysregulation of Cancer Hallmarks in Lower-Grade Glioma. PMID:34163522
Development and application of the ocular immune-mediated inflammatory diseases ontology enhanced with synonyms from online patient support forum conversation. PMID:34139439
Mapping the multiscale structure of biological systems. PMID:34139169
Network module-based drug repositioning for pulmonary arterial hypertension. PMID:34132494
Cruxome: a powerful tool for annotating, interpreting and reporting genetic variants. PMID:34082700
GCSENet: A GCN, CNN and SENet ensemble model for microRNA-disease association prediction. PMID:34081706
How to design a registry for undiagnosed patients in the framework of rare disease diagnosis: suggestions on software, data set and coding system. PMID:33933089
The VRNetzer platform enables interactive network analysis in Virtual Reality. PMID:33893283
Application and evaluation of knowledge graph embeddings in biomedical data. PMID:33816992
Molecular Profiling Reveals Involvement of ESCO2 in Intermediate Progenitor Cell Maintenance in the Developing Mouse Cortex. PMID:33798452
HPO-driven virtual gene panel: a new efficient approach in molecular autopsy of sudden unexplained death. PMID:33789662
Underrepresentation of Phenotypic Variability of 16p13.11 Microduplication Syndrome Assessed With an Online Self-Phenotyping Tool (Phenotypr): Cohort Study. PMID:33724192
Treat Iron-Related Childhood-Onset Neurodegeneration (TIRCON)-An International Network on Care and Research for Patients With Neurodegeneration With Brain Iron Accumulation (NBIA). PMID:33692746
RDmap: a map for exploring rare diseases. PMID:33632281
Human disease genes website series: An international, open and dynamic library for up-to-date clinical information. PMID:33439542
The case for open science: rare diseases. PMID:33426479
GeneBreaker: Variant simulation to improve the diagnosis of Mendelian rare genetic diseases. PMID:33368787
A flexible computational pipeline for research analyses of unsolved clinical exome cases. PMID:33303739
LZTR1-related spinal schwannomatosis and 7q11.23 duplication syndrome: A complex phenotype with dual diagnosis. PMID:33269527
COVID-19 Knowledge Extractor (COKE): A Tool and a Web Portal to Extract Drug - Target Protein Associations from the CORD-19 Corpus of Scientific Publications on COVID-19. PMID:33269341
The Human Phenotype Ontology in 2021. PMID:33264411
KG-COVID-19: A Framework to Produce Customized Knowledge Graphs for COVID-19 Response. PMID:33196056
Mapping scientific landscapes in UMLS research: a scientometric review. PMID:33059367
Predicting candidate genes from phenotypes, functions and anatomical site of expression. PMID:33051643
Semantic similarity and machine learning with ontologies. PMID:33049044
Practical guide to genetic screening for inherited eye diseases. PMID:33015543
Epidemiology of recurrent seizure disorders and epilepsy in cats under primary veterinary care in the United Kingdom. PMID:32974979
Deciphering the Underlying Mechanism of Eucommiae Cortex against Osteoporotic Fracture by Network Pharmacology. PMID:32963568
Systematic Review: Monoclonal Antibody-Induced Subacute Cutaneous Lupus Erythematosus. PMID:32960413
An interactive retrieval system for clinical trial studies with context-dependent protocol elements. PMID:32946464
Semantic Similarity Analysis Reveals Robust Gene-Disease Relationships in Developmental and Epileptic Encephalopathies. PMID:32853554
What You Need to Know Before Implementing a Clinical Research Data Warehouse: Comparative Review of Integrated Data Repositories in Health Care Institutions. PMID:32852280
KG-COVID-19: a framework to produce customized knowledge graphs for COVID-19 response. PMID:32839776
A longitudinal footprint of genetic epilepsies using automated electronic medical record interpretation. PMID:32773773
Interpretable Clinical Genomics with a Likelihood Ratio Paradigm. PMID:32755546
A Network Pharmacology Approach to Investigate the Active Compounds and Mechanisms of Musk for Ischemic Stroke. PMID:32714405
Developing an automated mechanism to identify medical articles from wikipedia for knowledge extraction. PMID:32693245
Children's rare disease cohorts: an integrative research and clinical genomics initiative. PMID:32655885
Whole-genome sequencing of patients with rare diseases in a national health system. PMID:32581362
The use of machine learning in rare diseases: a scoping review. PMID:32517778
Developing a FHIR-based Framework for Phenome Wide Association Studies: A Case Study with A Pan-Cancer Cohort. PMID:32477698
An Improved Phenotype-Driven Tool for Rare Mendelian Variant Prioritization: Benchmarking Exomiser on Real Patient Whole-Exome Data. PMID:32340307
VarFish: comprehensive DNA variant analysis for diagnostics and research. PMID:32338743
Diagnosis support systems for rare diseases: a scoping review. PMID:32299466
Electronic health records and polygenic risk scores for predicting disease risk. PMID:32235907
DISNET: a framework for extracting phenotypic disease information from public sources. PMID:32110491
Controllability analysis of molecular pathways points to proteins that control the entire interaction network. PMID:32076007
Significantly different clinical phenotypes associated with mutations in synthesis and transamidase+remodeling glycosylphosphatidylinositol (GPI)-anchor biosynthesis genes. PMID:32019583
Whole-exome sequencing identified a novel variant in an Iranian patient affected by pycnodysostosis. PMID:31944631
Novel eye genes systematically discovered through an integrated analysis of mouse transcriptomes and phenome. PMID:31934309
Evolving knowledge graph similarity for supervised learning in complex biomedical domains. PMID:31900127
Genepanel.iobio - an easy to use web tool for generating disease- and phenotype-associated gene lists. PMID:31829207
Formal axioms in biomedical ontologies improve analysis and interpretation of associated data. PMID:31821406
Genetic Modifiers at the Crossroads of Personalised Medicine for Haemoglobinopathies. PMID:31717530
Computational Methods for Identifying Similar Diseases. PMID:31678735
Data-driven method to enhance craniofacial and oral phenotype vocabularies. PMID:31668172
Bi-allelic Variants in METTL5 Cause Autosomal-Recessive Intellectual Disability and Microcephaly. PMID:31564433
Encoding Clinical Data with the Human Phenotype Ontology for Computational Differential Diagnostics. PMID:31479590
Why digital medicine depends on interoperability. PMID:31453374
Fully connecting the Observational Health Data Science and Informatics (OHDSI) initiative with the world of linked open data. PMID:31307128
Australian Genomics: A Federated Model for Integrating Genomics into Healthcare. PMID:31271757
HPO2Vec+: Leveraging heterogeneous knowledge resources to enrich node embeddings for the Human Phenotype Ontology. PMID:31255713
De Novo Variants in TAOK1 Cause Neurodevelopmental Disorders. PMID:31230721
PEDIA: prioritization of exome data by image analysis. PMID:31164752
PathoPhenoDB, linking human pathogens to their phenotypes in support of infectious disease research. PMID:31160594
Drug repositioning of herbal compounds via a machine-learning approach. PMID:31138103
A Recurrent Missense Variant in AP2M1 Impairs Clathrin-Mediated Endocytosis and Causes Developmental and Epileptic Encephalopathy. PMID:31104773
Specific phenotype semantics facilitate gene prioritization in clinical exome sequencing. PMID:31053788
Predicting disease-related phenotypes using an integrated phenotype similarity measurement based on HPO. PMID:30953559
Are innovation and new technologies in precision medicine paving a new era in patients centric care? PMID:30953518
Phenotypes associated with genes encoding drug targets are predictive of clinical trial side effects. PMID:30952858
Opportunities and Challenges for Molecular Understanding of Ciliopathies-The 100,000 Genomes Project. PMID:30915099
Collective influencers in protein interaction networks. PMID:30850642
Incorporating Knowledge-Driven Insights into a Collaborative Filtering Model to Facilitate the Differential Diagnosis of Rare Diseases. PMID:30815196
Ontology based text mining of gene-phenotype associations: application to candidate gene prediction. PMID:30809638
Rare disease knowledge enrichment through a data-driven approach. PMID:30764825
Precision epidemiology for infectious disease control. PMID:30728537
DeepPVP: phenotype-based prioritization of causative variants using deep learning. PMID:30727941
Context-sensitive network analysis identifies food metabolites associated with Alzheimer's disease: an exploratory study. PMID:30704467
Rapid and accurate interpretation of clinical exomes using Phenoxome: a computational phenotype-driven approach. PMID:30626929
Integrating ontologies of human diseases, phenotypes, and radiological diagnosis. PMID:30624645
Reforming disease classification system-are we there yet? PMID:30613605
Genetics of Human Primary Hypertension: Focus on Hormonal Mechanisms. PMID:30590482
Early-onset inflammatory bowel disease as a model disease to identify key regulators of immune homeostasis mechanisms. PMID:30565237
RDAD: A Machine Learning System to Support Phenotype-Based Rare Disease Diagnosis. PMID:30564269
Complexities of genetic diagnosis illustrated by an atypical case of congenital hypoplastic anemia. PMID:30559313
The Genetic Diagnosis of Neurodegenerative Diseases and Therapeutic Perspectives. PMID:30551598
Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. PMID:30476213
Variant information systems for precision oncology. PMID:30463544
Ontology-based validation and identification of regulatory phenotypes. PMID:30423068
Gene's hubs in retinal diseases: A retinal disease network. PMID:30417144
An online tool for measuring and visualizing phenotype similarities using HPO. PMID:30367579
Overview of the BioCreative VI text-mining services for Kinome Curation Track. PMID:30329035
Genetic variants in components of the NALCN-UNC80-UNC79 ion channel complex cause a broad clinical phenotype (NALCN channelopathies). PMID:30167850
An integrated clinical program and crowdsourcing strategy for genomic sequencing and Mendelian disease gene discovery. PMID:30131872
Fishing forward and reverse: Advances in zebrafish phenomics. PMID:30130581
Computational resources associating diseases with genotypes, phenotypes and exposures. PMID:30102366
HPO2GO: prediction of human phenotype ontology term associations for proteins using cross ontology annotation co-occurrences. PMID:30083448
Deep Phenotyping on Electronic Health Records Facilitates Genetic Diagnosis by Clinical Exomes. PMID:29961570
Targeted exome analysis identifies the genetic basis of disease in over 50% of patients with a wide range of ataxia-related phenotypes. PMID:29915382
Leveraging Collaborative Filtering to Accelerate Rare Disease Diagnosis. PMID:29854225
A new method to measure the semantic similarity from query phenotypic abnormalities to diseases based on the human phenotype ontology. PMID:29745853
X-linked intellectual disability update 2017. PMID:29696803
Measuring phenotype-phenotype similarity through the interactome. PMID:29671400
Massive mining of publicly available RNA-seq data from human and mouse. PMID:29636450
Evaluation of involved proteins in colon adenocarcinoma: an interactome analysis. PMID:29511483
Novel findings with reassessment of exome data: implications for validation testing and interpretation of genomic data. PMID:29389922
PhenoDis: a comprehensive database for phenotypic characterization of rare cardiac diseases. PMID:29370821
InfAcrOnt: calculating cross-ontology term similarities using information flow by a random walk. PMID:29363423
Tackling the challenges of matching biomedical ontologies. PMID:29335022
Characterization of glycosylphosphatidylinositol biosynthesis defects by clinical features, flow cytometry, and automated image analysis. PMID:29310717
Investigations on factors influencing HPO-based semantic similarity calculation. PMID:29297376
Interoperability of Disease Concepts in Clinical and Research Ontologies: Contrasting Coverage and Structure in the Disease Ontology and SNOMED CT. PMID:29295235
Trends in Fetal Medicine: A 10-Year Bibliometric Analysis of Prenatal Diagnosis. PMID:29295220
Phenotypic Analysis of Clinical Narratives Using Human Phenotype Ontology. PMID:29295162
A taxonomy has been developed for outcomes in medical research to help improve knowledge discovery. PMID:29288712
The retina/RPE proteome in chick myopia and hyperopia models: Commonalities with inherited and age-related ocular pathologies. PMID:29259393
Integrating phenotype ontologies with PhenomeNET. PMID:29258588
A Novel de novo FZD2 Mutation in a Patient with Autosomal Dominant Omodysplasia. PMID:29230162
Care and cost consequences of pediatric whole genome sequencing compared to chromosome microarray. PMID:29158552
eRAM: encyclopedia of rare disease annotations for precision medicine. PMID:29106618
Prediction of Human Phenotype Ontology terms by means of hierarchical ensemble methods. PMID:29025394
A new synonym-substitution method to enrich the human phenotype ontology. PMID:29017443
Comprehending the Health Informatics Spectrum: Grappling with System Entropy and Advancing Quality Clinical Research. PMID:28959687
Mimvec: a deep learning approach for analyzing the human phenome. PMID:28950906
Phelan-McDermid syndrome data network: Integrating patient reported outcomes with clinical notes and curated genetic reports. PMID:28862395
Classification and analysis of a large collection of in vivo bioassay descriptions. PMID:28678787
Whole Genome Sequencing Expands Diagnostic Utility and Improves Clinical Management in Pediatric Medicine. PMID:28567303
Leveraging multiple genomic data to prioritize disease-causing indels from exome sequencing data. PMID:28496131
International Cooperation to Enable the Diagnosis of All Rare Genetic Diseases. PMID:28475856
The physical characteristics of human proteins in different biological functions. PMID:28459865
The anatomy of phenotype ontologies: principles, properties and applications. PMID:28387809
[Computer-assisted diagnosis of rare diseases]. PMID:28364276
Apert syndrome with S252W FGFR2 mutation and characterization using Phenomizer: An Indian case report. PMID:28316926
Whole genome sequencing of one complex pedigree illustrates challenges with genomic medicine. PMID:28228131
Var2GO: a web-based tool for gene variants selection. PMID:28185576
Ontology-Driven Search and Triage: Design of a Web-Based Visual Interface for MEDLINE. PMID:28153818
Context-sensitive network-based disease genetics prediction and its implications in drug discovery. PMID:28062449
Resolution of Disease Phenotypes Resulting from Multilocus Genomic Variation. PMID:27959697
The Human Phenotype Ontology in 2017. PMID:27899602
Text mining resources for the life sciences. PMID:27888231
Knowledge Representation and Management: a Linked Data Perspective. PMID:27830248
Dione: An OWL representation of ICD-10-CM for classifying patients' diseases. PMID:27737720
OAHG: an integrated resource for annotating human genes with multi-level ontologies. PMID:27703231
Drug repurposing for glioblastoma based on molecular subtypes. PMID:27697594
Quantitative Proteomics of Sleep-Deprived Mouse Brains Reveals Global Changes in Mitochondrial Proteins. PMID:27684481
A Novel Drug-Mouse Phenotypic Similarity Method Detects Molecular Determinants of Drug Effects. PMID:27673331
Gene Ontology synonym generation rules lead to increased performance in biomedical concept recognition. PMID:27613112
Phenome-based gene discovery provides information about Parkinson's disease drug targets. PMID:27586503
Explorations to improve the completeness of exome sequencing. PMID:27568008
Towards precision medicine-based therapies for glioblastoma: interrogating human disease genomics and mouse phenotypes. PMID:27557118
The Current Landscape of Genetic Testing in Cardiovascular Malformations: Opportunities and Challenges. PMID:27504451
Distinct genetic architectures for syndromic and nonsyndromic congenital heart defects identified by exome sequencing. PMID:27479907
Network topology measures for identifying disease-gene association in breast cancer. PMID:27454166
A Comprehensive Evaluation of Disease Phenotype Networks for Gene Prioritization. PMID:27415759
An integer programming framework for inferring disease complexes from network data. PMID:27307626
DNetDB: The human disease network database based on dysfunctional regulation mechanism. PMID:27209279
Recommendations for the integration of genomics into clinical practice. PMID:27171546
Exome sequencing reveals two novel compound heterozygous XYLT1 mutations in a Polish patient with Desbuquois dysplasia type 2 and growth hormone deficiency. PMID:27030147
Linking MedDRA(®)-Coded Clinical Phenotypes to Biological Mechanisms by the Ontology of Adverse Events: A Pilot Study on Tyrosine Kinase Inhibitors. PMID:27003817
Systematic identification of phenotypically enriched loci using a patient network of genomic disorders. PMID:26980139
Merging Electronic Health Record Data and Genomics for Cardiovascular Research: A Science Advisory From the American Heart Association. PMID:26976545
Combining Human Disease Genetics and Mouse Model Phenotypes towards Drug Repositioning for Parkinson's disease. PMID:26958284
A dominant gain-of-function mutation in universal tyrosine kinase SRC causes thrombocytopenia, myelofibrosis, bleeding, and bone pathologies. PMID:26936507
Mutations in Subunits of the Activating Signal Cointegrator 1 Complex Are Associated with Prenatal Spinal Muscular Atrophy and Congenital Bone Fractures. PMID:26924529
Human Variome Project Quality Assessment Criteria for Variation Databases. PMID:26919176
A visual and curatorial approach to clinical variant prioritization and disease gene discovery in genome-wide diagnostics. PMID:26838676
Semantic representation of reported measurements in radiology. PMID:26801764
A network medicine approach to quantify distance between hereditary disease modules on the interactome. PMID:26631976
A generic solution for web-based management of pseudonymized data. PMID:26621059
Testing for Ancient Selection Using Cross-population Allele Frequency Differentiation. PMID:26596347
Next-generation diagnostics and disease-gene discovery with the Exomiser. PMID:26562621
Acquisition, Analysis, and Sharing of Data in 2015 and Beyond: A Survey of the Landscape: A Conference Report From the American Heart Association Data Summit 2015. PMID:26541391
Compound heterozygous mutations in the noncoding RNU4ATAC cause Roifman Syndrome by disrupting minor intron splicing. PMID:26522830
PhenoMiner: from text to a database of phenotypes associated with OMIM diseases. PMID:26507285
Standardized phenotyping enhances Mendelian disease gene identification. PMID:26506899
The human disease network in terms of dysfunctional regulatory mechanisms. PMID:26450611
Harmonising and linking biomedical and clinical data across disparate data archives to enable integrative cross-biobank research. PMID:26306643
Diagnostic interpretation of array data using public databases and internet sources. PMID:26285306
Utility of whole-exome sequencing for those near the end of the diagnostic odyssey: time to address gaps in care. PMID:26283276
Use of model organism and disease databases to support matchmaking for human disease gene discovery. PMID:26269093
GenomeConnect: matchmaking between patients, clinical laboratories, and researchers to improve genomic knowledge. PMID:26178529
How to build personalized multi-omics comorbidity profiles. PMID:26157799
PhenoPredict: A disease phenome-wide drug repositioning approach towards schizophrenia drug discovery. PMID:26151312
The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease. PMID:26119816
Phenome-driven disease genetics prediction toward drug discovery. PMID:26072493
De novo deletions and duplications of 17q25.3 cause susceptibility to cardiovascular malformations. PMID:26070612
Analysis of the human diseasome using phenotype similarity between common, genetic, and infectious diseases. PMID:26051359
Concept selection for phenotypes and diseases using learn to rank. PMID:26034558
Human phenotype ontology annotation and cluster analysis to unravel genetic defects in 707 cases with unexplained bleeding and platelet disorders. PMID:25949529
Capturing domain knowledge from multiple sources: the rare bone disorders use case. PMID:25926964
The clustering of functionally related genes contributes to CNV-mediated disease. PMID:25887030
Development and validation of a classification approach for extracting severity automatically from electronic health records. PMID:25848530
Gene networks underlying convergent and pleiotropic phenotypes in a large and systematically-phenotyped cohort with heterogeneous developmental disorders. PMID:25781962
Similarity-based search of model organism, disease and drug effect phenotypes. PMID:25763178
Automatic concept recognition using the human phenotype ontology reference and test suite corpora. PMID:25725061
Finding genetic overlaps among diseases based on ranked gene lists. PMID:25684200
HPOSim: an R package for phenotypic similarity measure and enrichment analysis based on the human phenotype ontology. PMID:25664462
Mosaic structural variation in children with developmental disorders. PMID:25634561
Prioritizing causal disease genes using unbiased genomic features. PMID:25633252
PhenomeExpress: a refined network analysis of expression datasets by inclusion of known disease phenotypes. PMID:25631385
Aber-OWL: a framework for ontology-based data access in biology. PMID:25627673
Phenomics research on coronary heart disease based on human phenotype ontology. PMID:25610858
Mutations in PTRH2 cause novel infantile-onset multisystem disease with intellectual disability, microcephaly, progressive ataxia, and muscle weakness. PMID:25574476
Finding our way through phenotypes. PMID:25562316
Homozygous and compound-heterozygous mutations in TGDS cause Catel-Manzke syndrome. PMID:25480037
PhenUMA: a tool for integrating the biomedical relationships among genes and diseases. PMID:25420641
Text mining in cancer gene and pathway prioritization. PMID:25392685
Screening for single nucleotide variants, small indels and exon deletions with a next-generation sequencing based gene panel approach for Usher syndrome. PMID:25333064
Large homozygous RAB3GAP1 gene microdeletion causes Warburg micro syndrome 1. PMID:25332050
Spotlite: web application and augmented algorithms for predicting co-complexed proteins from affinity purification--mass spectrometry data. PMID:25300367
Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome. PMID:25186178
Unbiased functional clustering of gene variants with a phenotypic-linkage network. PMID:25166029
Clinical phenotype-based gene prioritization: an initial study using semantic similarity and the human phenotype ontology. PMID:25047600
Network based integrated analysis of phenotype-genotype data for prioritization of candidate symptom genes. PMID:24991551
Correlating information contents of gene ontology terms to infer semantic similarity of gene products. PMID:24963342
Next-generation sequencing for research and diagnostics in kidney disease. PMID:24914583
Convergence of genes and cellular pathways dysregulated in autism spectrum disorders. PMID:24768552
Novel skin phenotypes revealed by a genome-wide mouse reverse genetic screen. PMID:24721909
Genetic profiling for risk reduction in human cardiovascular disease. PMID:24705294
Phevor combines multiple biomedical ontologies for accurate identification of disease-causing alleles in single individuals and small nuclear families. PMID:24702956
Phenotype ontologies and cross-species analysis for translational research. PMID:24699242
Integrating multiple genomic data to predict disease-causing nonsynonymous single nucleotide variants in exome sequencing studies. PMID:24651380
The automated function prediction SIG looks back at 2013 and prepares for 2014. PMID:24590444
Variation ontology: annotator guide. PMID:24533660
Semantic interestingness measures for discovering association rules in the skeletal dysplasia domain. PMID:24499729
Walking on a tissue-specific disease-protein-complex heterogeneous network for the discovery of disease-related protein complexes. PMID:24455720
The epidemiology ontology: an ontology for the semantic annotation of epidemiological resources. PMID:24438387
Annotating DNA variants is the next major goal for human genetics. PMID:24387988
OGA: an ontological tool of human phenotypes with genetic associations. PMID:24308566
ClinVar: public archive of relationships among sequence variation and human phenotype. PMID:24234437
The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. PMID:24217912
Human intellectual disability genes form conserved functional modules in Drosophila. PMID:24204314
Analyzing gene expression data in mice with the Neuro Behavior Ontology. PMID:24177753
Improved exome prioritization of disease genes through cross-species phenotype comparison. PMID:24162188
Variation Ontology for annotation of variation effects and mechanisms. PMID:24162187
Mouse model phenotypes provide information about human drug targets. PMID:24158600
Learning to recognize phenotype candidates in the auto-immune literature using SVM re-ranking. PMID:24155869
SIDD: a semantically integrated database towards a global view of human disease. PMID:24146757
Automatically transforming pre- to post-composed phenotypes: EQ-lising HPO and MP. PMID:24131519
Homozygous missense and nonsense mutations in BMPR1B cause acromesomelic chondrodysplasia-type Grebe. PMID:24129431
A GDF5 point mutation strikes twice--causing BDA1 and SYNS2. PMID:24098149
Toward knowledge support for analysis and interpretation of complex traits. PMID:24079802
eXtasy: variant prioritization by genomic data fusion. PMID:24076761
Rare-disease genetics in the era of next-generation sequencing: discovery to translation. PMID:23999272
Navigating traditional chinese medicine network pharmacology and computational tools. PMID:23983798
The Vertebrate Trait Ontology: a controlled vocabulary for the annotation of trait data across species. PMID:23937709
Estimating exome genotyping accuracy by comparing to data from large scale sequencing projects. PMID:23902830
An integrative, translational approach to understanding rare and orphan genetically based diseases. PMID:23853703
WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013. PMID:23703215
Molecular genetic testing and the future of clinical genomics. PMID:23681062
A two-level model for the analysis of syndrome of acute ischemic stroke: from diagnostic model to molecular mechanism. PMID:23662126
PhenoDigm: analyzing curated annotations to associate animal models with human diseases. PMID:23660285
GeneSetDB: A comprehensive meta-database, statistical and visualisation framework for gene set analysis. PMID:23650583
Chapter 15: disease gene prioritization. PMID:23633938
ZC4H2 mutations are associated with arthrogryposis multiplex congenita and intellectual disability through impairment of central and peripheral synaptic plasticity. PMID:23623388
MalaCards: an integrated compendium for diseases and their annotation. PMID:23584832
PGAP2 mutations, affecting the GPI-anchor-synthesis pathway, cause hyperphosphatasia with mental retardation syndrome. PMID:23561847
From ontology to semantic similarity: calculation of ontology-based semantic similarity. PMID:23533360
Doubly heterozygous LMNA and TTN mutations revealed by exome sequencing in a severe form of dilated cardiomyopathy. PMID:23463027
Decomposing phenotype descriptions for the human skeletal phenome. PMID:23440304
Global analysis of the human pathophenotypic similarity gene network merges disease module components. PMID:23437198
Mining skeletal phenotype descriptions from scientific literature. PMID:23409017
PhenoDB: a new web-based tool for the collection, storage, and analysis of phenotypic features. PMID:23378291
HDAM: a resource of human disease associated mutations from next generation sequencing studies. PMID:23369322
Semantically enabling a genome-wide association study database. PMID:23244533
Decision support methods for finding phenotype--disorder associations in the bone dysplasia domain. PMID:23226331
The NIH genetic testing registry: a new, centralized database of genetic tests to enable access to comprehensive information and improve transparency. PMID:23193275
DcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more. PMID:23161684
Linking genome annotation projects with genetic disorders using ontologies. PMID:23149630
Phenotypic overlap in the contribution of individual genes to CNV pathogenicity revealed by cross-species computational analysis of single-gene mutations in humans, mice and zebrafish. PMID:23104991
A clinical evaluation tool for SNP arrays, especially for autosomal recessive conditions in offspring of consanguineous parents. PMID:23100014
Supervised segmentation of phenotype descriptions for the human skeletal phenome using hybrid methods. PMID:23061930
Continuation-like semantics for modeling structural process anomalies. PMID:23046705
Ontology-based cross-species integration and analysis of Saccharomyces cerevisiae phenotypes. PMID:23046642
Towards improving phenotype representation in OWL. PMID:23046625
Quantitative comparison of mapping methods between Human and Mammalian Phenotype Ontology. PMID:23046555
Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models. PMID:23033316
Annotate-it: a Swiss-knife approach to annotation, analysis and interpretation of single nucleotide variation in human disease. PMID:23013645
Sequence thyself: personalized medicine and therapies for the future: 2012 Yale Healthcare Conference. PMID:23012590
The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data. PMID:22961259
Querying phenotype-genotype relationships on patient datasets using semantic web technology: the example of Cerebrotendinous xanthomatosis. PMID:22849591
Bayesian ontology querying for accurate and noise-tolerant semantic searches. PMID:22843981
Identifying disease mutations in genomic medicine settings: current challenges and how to accelerate progress. PMID:22830651
Network medicine: linking disorders. PMID:22825316
Computational tools for comparative phenomics: the role and promise of ontologies. PMID:22814867
Differential functional constraints on the evolution of postsynaptic density proteins in neocortical laminae. PMID:22761869
Computational tools for prioritizing candidate genes: boosting disease gene discovery. PMID:22751426
Improving disease gene prioritization by comparing the semantic similarity of phenotypes in mice with those of human diseases. PMID:22719993
Identifying aberrant pathways through integrated analysis of knowledge in pharmacogenomics. PMID:22711793
The laboratory-clinician team: a professional call to action to improve communication and collaboration for optimal patient care in chromosomal microarray testing. PMID:22610653
Semantic integration of physiology phenotypes with an application to the Cellular Phenotype Ontology. PMID:22539675
The Bone Dysplasia Ontology: integrating genotype and phenotype information in the skeletal dysplasia domain. PMID:22449239
Mouse genetic and phenotypic resources for human genetics. PMID:22422677
Phenotypic information in genomic variant databases enhances clinical care and research: the International Standards for Cytogenomic Arrays Consortium experience. PMID:22331816
MouseFinder: Candidate disease genes from mouse phenotype data. PMID:22331800
Uberon, an integrative multi-species anatomy ontology. PMID:22293552
Semantically enabling pharmacogenomic data for the realization of personalized medicine. PMID:22256869
Similarity-based disease risk assessment for personal genomes: proof of concept. PMID:22195217
GWASdb: a database for human genetic variants identified by genome-wide association studies. PMID:22139925
Exact score distribution computation for ontological similarity searches. PMID:22078312
Improving ontologies by automatic reasoning and evaluation of logical definitions. PMID:22032770
Exploring the elephant: histopathology in high-throughput phenotyping of mutant mice. PMID:22028326
An ontologically founded architecture for information systems in clinical and epidemiological research. PMID:21995847
New approaches to the representation and analysis of phenotype knowledge in human diseases and their animal models. PMID:21987712
Prioritizing human cancer microRNAs based on genes' functional consistency between microRNA and cancer. PMID:21976726
Interoperability between biomedical ontologies through relation expansion, upper-level ontologies and automatic reasoning. PMID:21789201
PhenomeNET: a whole-phenome approach to disease gene discovery. PMID:21737429
PREDICT: a method for inferring novel drug indications with application to personalized medicine. PMID:21654673
Towards an Age-Phenome Knowledge-base. PMID:21651792
Call for participation in the neurogenetics consortium within the Human Variome Project. PMID:21630033
DomainRBF: a Bayesian regression approach to the prioritization of candidate domains for complex diseases. PMID:21504591
The FaceBase Consortium: a comprehensive program to facilitate craniofacial research. PMID:21458441
Transactional database transformation and its application in prioritizing human disease genes. PMID:21422495
CSI-OMIM--Clinical Synopsis Search in OMIM. PMID:21362185
A common layer of interoperability for biomedical ontologies based on OWL EL. PMID:21343142
Worm Phenotype Ontology: integrating phenotype data within and beyond the C. elegans community. PMID:21261995
Characterization of the proteome, diseases and evolution of the human postsynaptic density. PMID:21170055
Laboratory mouse models for the human genome-wide associations. PMID:21072174
SUPERFAMILY 1.75 including a domain-centric gene ontology method. PMID:21062816
Interoperability between phenotype and anatomy ontologies. PMID:20971987
Improving disease gene prioritization using the semantic similarity of Gene Ontology terms. PMID:20823322
Commentary: mouse genetic nomenclature. Standardization of strain, gene, and protein symbols. PMID:20685919
Applying the functional abnormality ontology pattern to anatomical functions. PMID:20618982
Semi-automated ontology generation within OBO-Edit. PMID:20529942
PhenoHM: human-mouse comparative phenome-genome server. PMID:20507906
Phenotype ontologies for mouse and man: bridging the semantic gap. PMID:20427557
Towards the integration of mouse databases - definition and implementation of solutions to two use-cases in mouse functional genomics. PMID:20205870
Easy retrieval of single amino-acid polymorphisms and phenotype information using SwissVar. PMID:20106818
Integrating phenotype ontologies across multiple species. PMID:20064205
The mammalian phenotype ontology: enabling robust annotation and comparative analysis. PMID:20052305
The biological coherence of human phenome databases. PMID:20004759
Entity/quality-based logical definitions for the human skeletal phenome using PATO. PMID:19964203
Linking human diseases to animal models using ontology-based phenotype annotation. PMID:19956802
Clinical diagnostics in human genetics with semantic similarity searches in ontologies. PMID:19800049
SimCT: a generic tool to visualize ontology-based relationships for biological objects. PMID:19776214
Between proteins and phenotypes: annotation and interpretation of mutations. PMID:19758463
Phenotypic categorization of genetic skin diseases reveals new relations between phenotypes, genes and pathways. PMID:19744994
Linking genes to diseases: it's all in the data. PMID:19678910
Mouse, man, and meaning: bridging the semantics of mouse phenotype and human disease. PMID:19649761
Translational disease interpretation with molecular networks. PMID:19591646
CA8 mutations cause a novel syndrome characterized by ataxia and mild mental retardation with predisposition to quadrupedal gait. PMID:19461874
The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data PubMed citations: 353.

353 articles citing: The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data

Promoter/enhancer-based controllability of regulatory networks. PMID:35241702
Computational Genomics in the Era of Precision Medicine: Applications to Variant Analysis and Gene Therapy. PMID:35207663
Epigenomic Modifications in Modern and Ancient Genomes. PMID:35205223
Evaluating semantic similarity methods for comparison of text-derived phenotype profiles. PMID:35123470
Novel compound heterozygous variants in XYLT1 gene caused Desbuquois dysplasia type 2 in an aborted fetus: a case report. PMID:35081921
Diagnosis of Genetic White Matter Disorders by Singleton Whole-Exome and Genome Sequencing Using Interactome-Driven Prioritization. PMID:35012964
Concept recognition as a machine translation problem. PMID:34920707
FAIR data representation in times of eScience: a comparison of instance-based and class-based semantic representations of empirical data using phenotype descriptions as example. PMID:34823588
Network analysis reveals rare disease signatures across multiple levels of biological organization. PMID:34753928
Use of whole genome sequencing to determine genetic basis of suspected mitochondrial disorders: cohort study. PMID:34732400
Deep semi-supervised learning ensemble framework for classifying co-mentions of human proteins and phenotypes. PMID:34656098
CADA: phenotype-driven gene prioritization based on a case-enriched knowledge graph. PMID:34514393
Breast tumor stiffness instructs bone metastasis via maintenance of mechanical conditioning. PMID:34192535
Clinical and molecular characterization of craniofrontonasal syndrome: new symptoms and novel pathogenic variants in the EFNB1 gene. PMID:34174922
Cruxome: a powerful tool for annotating, interpreting and reporting genetic variants. PMID:34082700
Lantern: an integrative repository of functional annotations for lncRNAs in the human genome. PMID:34039271
WEScover: selection between clinical whole exome sequencing and gene panel testing. PMID:34016036
An overview of graph databases and their applications in the biomedical domain. PMID:34003247
hu.MAP 2.0: integration of over 15,000 proteomic experiments builds a global compendium of human multiprotein assemblies. PMID:33973408
The cis-regulatory effects of modern human-specific variants. PMID:33885362
Improved characterisation of clinical text through ontology-based vocabulary expansion. PMID:33845909
Towards similarity-based differential diagnostics for common diseases. PMID:33836447
Application and evaluation of knowledge graph embeddings in biomedical data. PMID:33816992
HPO-driven virtual gene panel: a new efficient approach in molecular autopsy of sudden unexplained death. PMID:33789662
Human-chimpanzee fused cells reveal cis-regulatory divergence underlying skeletal evolution. PMID:33731941
Underrepresentation of Phenotypic Variability of 16p13.11 Microduplication Syndrome Assessed With an Online Self-Phenotyping Tool (Phenotypr): Cohort Study. PMID:33724192
RDmap: a map for exploring rare diseases. PMID:33632281
A fast, accurate, and generalisable heuristic-based negation detection algorithm for clinical text. PMID:33484944
Male pseudohermaphroditism: A case study of 46,XY disorder of sexual development using whole-exome sequencing. PMID:33363845
Towards semantic interoperability: finding and repairing hidden contradictions in biomedical ontologies. PMID:33319712
PathExt: a general framework for path-based mining of omics-integrated biological networks. PMID:33305329
The Human Phenotype Ontology in 2021. PMID:33264411
An integrative knowledge graph for rare diseases, derived from the Genetic and Rare Diseases Information Center (GARD). PMID:33183351
Evaluating variants classified as pathogenic in ClinVar in the DDD Study. PMID:33149276
Clinical sites of the Undiagnosed Diseases Network: unique contributions to genomic medicine and science. PMID:33093671
The GTEx Consortium atlas of genetic regulatory effects across human tissues. PMID:32913098
Semantic Similarity Analysis Reveals Robust Gene-Disease Relationships in Developmental and Epileptic Encephalopathies. PMID:32853554
Network study of nasal transcriptome profiles reveals master regulator genes of asthma. PMID:32828590
Interpretable Clinical Genomics with a Likelihood Ratio Paradigm. PMID:32755546
UFO: A tool for unifying biomedical ontology-based semantic similarity calculation, enrichment analysis and visualization. PMID:32645039
Mutational and phenotypic characterization of hereditary hemorrhagic telangiectasia. PMID:32573726
A high-coverage Neandertal genome from Chagyrskaya Cave. PMID:32546518
Atomic-resolution mapping of transcription factor-DNA interactions by femtosecond laser crosslinking and mass spectrometry. PMID:32541649
Unblending of Transcriptional Condensates in Human Repeat Expansion Disease. PMID:32386547
Pathogenic variants in KPTN gene identified by clinical whole-genome sequencing. PMID:32358097
An Improved Phenotype-Driven Tool for Rare Mendelian Variant Prioritization: Benchmarking Exomiser on Real Patient Whole-Exome Data. PMID:32340307
Clinical Integration of Genome Diagnostics for Congenital Anomalies of the Kidney and Urinary Tract. PMID:32312792
BioHackathon 2015: Semantics of data for life sciences and reproducible research. PMID:32308977
Integrated querying and version control of context-specific biological networks. PMID:32294194
TarGo: network based target gene selection system for human disease related mouse models. PMID:32257911
Differential DNA methylation of vocal and facial anatomy genes in modern humans. PMID:32132541
Genome sequencing identifies a homozygous inversion disrupting QDPR as a cause for dihydropteridine reductase deficiency. PMID:32022462
Significantly different clinical phenotypes associated with mutations in synthesis and transamidase+remodeling glycosylphosphatidylinositol (GPI)-anchor biosynthesis genes. PMID:32019583
Review-Current Concepts in Inflammatory Skin Diseases Evolved by Transcriptome Analysis: In-Depth Analysis of Atopic Dermatitis and Psoriasis. PMID:31973112
Human protein-RNA interaction network is highly stable across mammals. PMID:31888461
HPOAnnotator: improving large-scale prediction of HPO annotations by low-rank approximation with HPO semantic similarities and multiple PPI networks. PMID:31865916
GTX.Digest.VCF: an online NGS data interpretation system based on intelligent gene ranking and large-scale text mining. PMID:31856831
Using mechanistic models for the clinical interpretation of complex genomic variation. PMID:31831811
Cardioinformatics: the nexus of bioinformatics and precision cardiology. PMID:31802103
DAISY: A Data Information System for accountability under the General Data Protection Regulation. PMID:31800037
Standard operating procedure for curation and clinical interpretation of variants in cancer. PMID:31779674
Personalised analytics for rare disease diagnostics. PMID:31754101
Genetic Modifiers at the Crossroads of Personalised Medicine for Haemoglobinopathies. PMID:31717530
A Combined Multi-Cohort Approach Reveals Novel and Known Genome-Wide Selection Signatures for Wool Traits in Merino and Merino-Derived Sheep Breeds. PMID:31708969
From cytogenetics to cytogenomics: whole-genome sequencing as a first-line test comprehensively captures the diverse spectrum of disease-causing genetic variation underlying intellectual disability. PMID:31694722
Matching whole genomes to rare genetic disorders: Identification of potential causative variants using phenotype-weighted knowledge in the CAGI SickKids5 clinical genomes challenge. PMID:31680375
ColPortal, an integrative multiomic platform for analysing epigenetic interactions in colorectal cancer. PMID:31672979
Data-driven method to enhance craniofacial and oral phenotype vocabularies. PMID:31668172
Finding Diagnostically Useful Patterns in Quantitative Phenotypic Data. PMID:31607427
Debutant iOS app and gene-disease complexities in clinical genomics and precision medicine. PMID:31586224
Genomics of rare genetic diseases-experiences from India. PMID:31554517
A Survey of Gene Prioritization Tools for Mendelian and Complex Human Diseases. PMID:31494632
Encoding Clinical Data with the Human Phenotype Ontology for Computational Differential Diagnostics. PMID:31479590
Integrative transcriptome imputation reveals tissue-specific and shared biological mechanisms mediating susceptibility to complex traits. PMID:31444360
HPO-Shuffle: an associated gene prioritization strategy and its application in drug repurposing for the treatment of canine epilepsy. PMID:31427480
Ontology-based venous thromboembolism risk assessment model developing from medical records. PMID:31391095
Fetal phenotypes emerge as genetic technologies become robust. PMID:31330568
Clinically-relevant postzygotic mosaicism in parents and children with developmental disorders in trio exome sequencing data. PMID:31278258
Vitamin D3-vitamin D receptor axis suppresses pulmonary emphysema by maintaining alveolar macrophage homeostasis and function. PMID:31278070
Extracting Biomedical Terms from Postpartum Depression Online Health Communities. PMID:31259014
Analysis of disease organ as a novel phenotype towards disease genetics understanding. PMID:31207382
An Effective Method to Measure Disease Similarity Using Gene and Phenotype Associations. PMID:31164903
Flexible and scalable diagnostic filtering of genomic variants using G2P with Ensembl VEP. PMID:31147538
Personalized medicine-concepts, technologies, and applications in inflammatory skin diseases. PMID:31124204
Exome Sequencing in Children. PMID:31056085
Expanding the neurodevelopmental phenotypes of individuals with de novo KMT2A variants. PMID:31044088
The multiplex network of human diseases. PMID:31044086
eDiVA-Classification and prioritization of pathogenic variants for clinical diagnostics. PMID:31026367
Curating gene sets: challenges and opportunities for integrative analysis. PMID:30888410
Rare disease knowledge enrichment through a data-driven approach. PMID:30764825
A semiautomated whole-exome sequencing workflow leads to increased diagnostic yield and identification of novel candidate variants. PMID:30755392
DeepPVP: phenotype-based prioritization of causative variants using deep learning. PMID:30727941
Insights into genetics, human biology and disease gleaned from family based genomic studies. PMID:30655598
Using the drug-protein interactome to identify anti-ageing compounds for humans. PMID:30625143
Integrating ontologies of human diseases, phenotypes, and radiological diagnosis. PMID:30624645
Ensembl variation resources. PMID:30576484
Cardiac function evaluation for a novel one-step detoxification product of Aconiti Lateralis Radix Praeparata. PMID:30568725
iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data. PMID:30567491
The Genetic Diagnosis of Neurodegenerative Diseases and Therapeutic Perspectives. PMID:30551598
MER: a shell script and annotation server for minimal named entity recognition and linking. PMID:30519990
Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. PMID:30476213
Comparative expression profiling reveals widespread coordinated evolution of gene expression across eukaryotes. PMID:30470754
funcExplorer: a tool for fast data-driven functional characterisation of high-throughput expression data. PMID:30428831
Semantic Disease Gene Embeddings (SmuDGE): phenotype-based disease gene prioritization without phenotypes. PMID:30423077
Genotype and phenotype variability in Sjögren-Larsson syndrome. PMID:30372562
The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. PMID:30371894
An online tool for measuring and visualizing phenotype similarities using HPO. PMID:30367579
The ClinGen Epilepsy Gene Curation Expert Panel-Bridging the divide between clinical domain knowledge and formal gene curation criteria. PMID:30311377
A survey of ontology learning techniques and applications. PMID:30295720
Phenotype-Specific Enrichment of Mendelian Disorder Genes near GWAS Regions across 62 Complex Traits. PMID:30290150
Clinical exome sequencing for fetuses with ultrasound abnormalities and a suspected Mendelian disorder. PMID:30266093
Meeting Patients' Right to the Correct Diagnosis: Ongoing International Initiatives on Undiagnosed Rare Diseases and Ethical and Social Issues. PMID:30248891
Eight years after an international workshop on myotonic dystrophy patient registries: case study of a global collaboration for a rare disease. PMID:30185236
An integrated clinical program and crowdsourcing strategy for genomic sequencing and Mendelian disease gene discovery. PMID:30131872
Computational resources associating diseases with genotypes, phenotypes and exposures. PMID:30102366
Computational Prediction of Position Effects of Human Chromosome Rearrangements. PMID:30038699
[From symptom to syndrome using modern software support]. PMID:29995249
Phenotype-loci associations in networks of patients with rare disorders: application to assist in the diagnosis of novel clinical cases. PMID:29946186
CogStack - experiences of deploying integrated information retrieval and extraction services in a large National Health Service Foundation Trust hospital. PMID:29941004
Network-based machine learning and graph theory algorithms for precision oncology. PMID:29872707
VarAFT: a variant annotation and filtration system for human next generation sequencing data. PMID:29860484
A new method to measure the semantic similarity from query phenotypic abnormalities to diseases based on the human phenotype ontology. PMID:29745853
Improved ontology-based similarity calculations using a study-wise annotation model. PMID:29688377
A Systems Approach to Refine Disease Taxonomy by Integrating Phenotypic and Molecular Networks. PMID:29669699
Biocuration: Distilling data into knowledge. PMID:29659566
Deep learning meets ontologies: experiments to anchor the cardiovascular disease ontology in the biomedical literature. PMID:29650041
Phenotype risk scores identify patients with unrecognized Mendelian disease patterns. PMID:29590070
Where to search top-K biomedical ontologies? PMID:29579141
Whole-genome sequencing of Atacama skeleton shows novel mutations linked with dysplasia. PMID:29567674
A phenotype centric benchmark of variant prioritisation tools. PMID:29423277
Estimating the mutational load for cardiovascular diseases in Pakistani population. PMID:29420653
Paediatric genomics: diagnosing rare disease in children. PMID:29398702
The RD-Connect Registry & Biobank Finder: a tool for sharing aggregated data and metadata among rare disease researchers. PMID:29396563
PhenoDis: a comprehensive database for phenotypic characterization of rare cardiac diseases. PMID:29370821
InfAcrOnt: calculating cross-ontology term similarities using information flow by a random walk. PMID:29363423
PhenoRank: reducing study bias in gene prioritization through simulation. PMID:29360927
Making new genetic diagnoses with old data: iterative reanalysis and reporting from genome-wide data in 1,133 families with developmental disorders. PMID:29323667
Improving the interoperability of biomedical ontologies with compound alignments. PMID:29316968
Putative functional genes in idiopathic dilated cardiomyopathy. PMID:29311597
A network-based meta-analysis for characterizing the genetic landscape of human aging. PMID:29270911
Clinical detection of deletion structural variants in whole-genome sequences. PMID:29263817
Integrating phenotype ontologies with PhenomeNET. PMID:29258588
Noncoding copy-number variations are associated with congenital limb malformation. PMID:29236091
BioSearch: a semantic search engine for Bio2RDF. PMID:29220451
Patients with rare diseases: from therapeutic orphans to pioneers of personalized treatments. PMID:29180354
The International Rare Diseases Research Consortium: Policies and Guidelines to maximize impact. PMID:29158551
Rare genetic variants in the endocannabinoid system genes CNR1 and DAGLA are associated with neurological phenotypes in humans. PMID:29145497
Diverse type 2 diabetes genetic risk factors functionally converge in a phenotype-focused gene network. PMID:29059180
A new synonym-substitution method to enrich the human phenotype ontology. PMID:29017443
Protein structure and phenotypic analysis of pathogenic and population missense variants in STXBP1. PMID:28944233
Mouse Genome Informatics (MGI) Resource: Genetic, Genomic, and Biological Knowledgebase for the Laboratory Mouse. PMID:28838066
Comprehensive Analysis of Tissue-wide Gene Expression and Phenotype Data Reveals Tissues Affected in Rare Genetic Disorders. PMID:28822752
Leveraging network analytics to infer patient syndrome and identify causal genes in rare disease cases. PMID:28812537
Genome-wide signatures of complex introgression and adaptive evolution in the big cats. PMID:28776029
Computational Prediction of Position Effects of Apparently Balanced Human Chromosomal Rearrangements. PMID:28735859
Knowledge base and mini-expert platform for the diagnosis of inborn errors of metabolism. PMID:28726811
Factors affecting interactome-based prediction of human genes associated with clinical signs. PMID:28715999
Evaluating phecodes, clinical classification software, and ICD-9-CM codes for phenome-wide association studies in the electronic health record. PMID:28686612
Disease Compass- a navigation system for disease knowledge based on ontology and linked data techniques. PMID:28629436
MyGeneFriends: A Social Network Linking Genes, Genetic Diseases, and Researchers. PMID:28623182
Defining Disease, Diagnosis, and Translational Medicine within a Homeostatic Perturbation Paradigm: The National Institutes of Health Undiagnosed Diseases Program Experience. PMID:28603714
Genomic diagnosis for children with intellectual disability and/or developmental delay. PMID:28554332
GLADIATOR: a global approach for elucidating disease modules. PMID:28549478
A pipeline combining multiple strategies for prioritizing heterozygous variants for the identification of candidate genes in exome datasets. PMID:28532469
CAGI4 SickKids clinical genomes challenge: A pipeline for identifying pathogenic variants. PMID:28512736
Successful Application of Whole Genome Sequencing in a Medical Genetics Clinic. PMID:28496993
International Cooperation to Enable the Diagnosis of All Rare Genetic Diseases. PMID:28475856
Use of Biomedical Ontologies for Integration of Biological Knowledge for Learning and Prediction of Adverse Drug Reactions. PMID:28469412
QueryOR: a comprehensive web platform for genetic variant analysis and prioritization. PMID:28454514
Towards a global cancer knowledge network: dissecting the current international cancer genomic sequencing landscape. PMID:28453708
Neuro-symbolic representation learning on biological knowledge graphs. PMID:28449114
Gene ORGANizer: linking genes to the organs they affect. PMID:28444223
Semantic prioritization of novel causative genomic variants. PMID:28414800
The anatomy of phenotype ontologies: principles, properties and applications. PMID:28387809
[Computer-assisted diagnosis of rare diseases]. PMID:28364276
Seten: a tool for systematic identification and comparison of processes, phenotypes, and diseases associated with RNA-binding proteins from condition-specific CLIP-seq profiles. PMID:28336542
A novel recessive TTN founder variant is a common cause of distal myopathy in the Serbian population. PMID:28295036
GT2RDF: Semantic Representation of Genetic Testing Data. PMID:28269903
Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder. PMID:28263302
Genomic variants reveal differential evolutionary constraints on human transglutaminases and point towards unrecognized significance of transglutaminase 2. PMID:28248968
Whole genome sequencing of one complex pedigree illustrates challenges with genomic medicine. PMID:28228131
Predicting disease-related genes using integrated biomedical networks. PMID:28198675
Evaluating the effect of annotation size on measures of semantic similarity. PMID:28193260
Opportunities and challenges of whole-genome and -exome sequencing. PMID:28193154
Var2GO: a web-based tool for gene variants selection. PMID:28185576
Dosage sensitivity is a major determinant of human copy number variant pathogenicity. PMID:28176757
The Undiagnosed Diseases Network: Accelerating Discovery about Health and Disease. PMID:28157539
Global inference of disease-causing single nucleotide variants from exome sequencing data. PMID:28155632
Loss-of-function mutations in the ATP13A2/PARK9 gene cause complicated hereditary spastic paraplegia (SPG78). PMID:28137957
A comprehensive global genotype-phenotype database for rare diseases. PMID:28116331
Context-sensitive network-based disease genetics prediction and its implications in drug discovery. PMID:28062449
ontologyX: a suite of R packages for working with ontological data. PMID:28062448
Structural analysis of pathogenic mutations in the DYRK1A gene in patients with developmental disorders. PMID:28053047
Identification of disease comorbidity through hidden molecular mechanisms. PMID:27991583
Leigh map: A novel computational diagnostic resource for mitochondrial disease. PMID:27977873
XGR software for enhanced interpretation of genomic summary data, illustrated by application to immunological traits. PMID:27964755
Resolution of Disease Phenotypes Resulting from Multilocus Genomic Variation. PMID:27959697
PCAN: phenotype consensus analysis to support disease-gene association. PMID:27923364
Function-driven discovery of disease genes in zebrafish using an integrated genomics big data resource. PMID:27903883
Open Targets: a platform for therapeutic target identification and validation. PMID:27899665
The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species. PMID:27899636
MalaCards: an amalgamated human disease compendium with diverse clinical and genetic annotation and structured search. PMID:27899610
The Human Phenotype Ontology in 2017. PMID:27899602
Ensembl 2017. PMID:27899575
Mouse Genome Database (MGD)-2017: community knowledge resource for the laboratory mouse. PMID:27899570
Genome, transcriptome and proteome: the rise of omics data and their integration in biomedical sciences. PMID:27881428
The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants. PMID:27842607
The genomic landscape of balanced cytogenetic abnormalities associated with human congenital anomalies. PMID:27841880
Efficient Results in Semantic Interoperability for Health Care. Findings from the Section on Knowledge Representation and Management. PMID:27830249
The Pre-Eclampsia Ontology: A Disease Ontology Representing the Domain Knowledge Specific to Pre-Eclampsia. PMID:27788142
Distributed Cognition and Process Management Enabling Individualized Translational Research: The NIH Undiagnosed Diseases Program Experience. PMID:27785453
'IRDiRC Recognized Resources': a new mechanism to support scientists to conduct efficient, high-quality research for rare diseases. PMID:27782107
OAHG: an integrated resource for annotating human genes with multi-level ontologies. PMID:27703231
Genome-wide compendium and functional assessment of in vivo heart enhancers. PMID:27703156
An information model for computable cancer phenotypes. PMID:27629872
Phenome-based gene discovery provides information about Parkinson's disease drug targets. PMID:27586503
Skeleton Genetics: a comprehensive database for genes and mutations related to genetic skeletal disorders. PMID:27580923
Fusing literature and full network data improves disease similarity computation. PMID:27578323
Insight: An ontology-based integrated database and analysis platform for epilepsy self-management research. PMID:27573308
A Whole-Genome Analysis Framework for Effective Identification of Pathogenic Regulatory Variants in Mendelian Disease. PMID:27569544
Explorations to improve the completeness of exome sequencing. PMID:27568008
Computer-assisted initial diagnosis of rare diseases. PMID:27547534
Navigating the Phenotype Frontier: The Monarch Initiative. PMID:27516611
The Current Landscape of Genetic Testing in Cardiovascular Malformations: Opportunities and Challenges. PMID:27504451
Deciphering Variability of PKD1 and PKD2 in an Italian Cohort of 643 Patients with Autosomal Dominant Polycystic Kidney Disease (ADPKD). PMID:27499327
A method for exploring implicit concept relatedness in biomedical knowledge network. PMID:27454167
Environmentally induced return to juvenile-like chemosensitivity in the respiratory control system of adult bullfrog, Lithobates catesbeianus. PMID:27444338
Systematic reanalysis of clinical exome data yields additional diagnoses: implications for providers. PMID:27441994
The Undiagnosed Diseases Program Integrated Collaboration System (UDPICS): One Program's Experience Developing Custom Software to Support Research for Complex-Disease Families. PMID:27417368
Estrogen-related receptor gamma implicated in a phenotype including hearing loss and mild developmental delay. PMID:27381092
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. PMID:27374120
Defining the Clinical Value of a Genomic Diagnosis in the Era of Next-Generation Sequencing. PMID:27362341
Inherited platelet disorders: Insight from platelet genomics using next-generation sequencing. PMID:27348543
DermO; an ontology for the description of dermatologic disease. PMID:27296450
Dysregulated signaling hubs of liver lipid metabolism reveal hepatocellular carcinoma pathogenesis. PMID:27216817
DNetDB: The human disease network database based on dysfunctional regulation mechanism. PMID:27209279
Recommendations for the integration of genomics into clinical practice. PMID:27171546
First applications of a targeted exome sequencing approach in fetuses with ultrasound abnormalities reveals an important fraction of cases with associated gene defects. PMID:27168972
Facilitating a culture of responsible and effective sharing of cancer genome data. PMID:27149219
Exome sequencing results in successful riboflavin treatment of a rapidly progressive neurological condition. PMID:27148561
Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. PMID:27141961
Advances in understanding - genetic basis of intellectual disability. PMID:27127621
Germline De Novo Mutations in GNB1 Cause Severe Neurodevelopmental Disability, Hypotonia, and Seizures. PMID:27108799
g:Profiler-a web server for functional interpretation of gene lists (2016 update). PMID:27098042
Inherited platelet disorders: toward DNA-based diagnosis. PMID:27095789
Novel bioinformatic developments for exome sequencing. PMID:27075447
Representing vision and blindness. PMID:27034769
Limb-girdle muscular dystrophies - international collaborations for translational research. PMID:27033376
Exome sequencing reveals two novel compound heterozygous XYLT1 mutations in a Polish patient with Desbuquois dysplasia type 2 and growth hormone deficiency. PMID:27030147
Utilizing a structural meta-ontology for family-based quality assurance of the BioPortal ontologies. PMID:26988001
Rare loss-of-function variants in SETD1A are associated with schizophrenia and developmental disorders. PMID:26974950
LORD: a phenotype-genotype semantically integrated biomedical data tool to support rare disease diagnosis coding in health information systems. PMID:26958175
Phenotype Similarity Regression for Identifying the Genetic Determinants of Rare Diseases. PMID:26924528
MSeqDR: A Centralized Knowledge Repository and Bioinformatics Web Resource to Facilitate Genomic Investigations in Mitochondrial Disease. PMID:26919060
Unravelling the human genome-phenome relationship using phenome-wide association studies. PMID:26875678
Laying a Community-Based Foundation for Data-Driven Semantic Standards in Environmental Health Sciences. PMID:26871594
Interoperability between phenotypes in research and healthcare terminologies--Investigating partial mappings between HPO and SNOMED CT. PMID:26865946
Weighting sequence variants based on their annotation increases power of whole-genome association studies. PMID:26854916
A review of the new HGNC gene family resource. PMID:26842383
A visual and curatorial approach to clinical variant prioritization and disease gene discovery in genome-wide diagnostics. PMID:26838676
PHENOstruct: Prediction of human phenotype ontology terms using heterogeneous data sources. PMID:26834980
Semantic interrogation of a multi knowledge domain ontological model of tendinopathy identifies four strong candidate risk genes. PMID:26804977
Consent Codes: Upholding Standard Data Use Conditions. PMID:26796797
A Factor Graph Approach to Automated GO Annotation. PMID:26771463
Systematic Phenomics Analysis Deconvolutes Genes Mutated in Intellectual Disability into Biologically Coherent Modules. PMID:26748517
"Reverse Genomics" Predicts Function of Human Conserved Noncoding Elements. PMID:26744417
Integrating population variation and protein structural analysis to improve clinical interpretation of missense variation: application to the WD40 domain. PMID:26740553
Emerging semantics to link phenotype and environment. PMID:26713234
Whole-Exome Sequencing and Whole-Genome Sequencing in Critically Ill Neonates Suspected to Have Single-Gene Disorders. PMID:26684335
TAF1 Variants Are Associated with Dysmorphic Features, Intellectual Disability, and Neurological Manifestations. PMID:26637982
Molecular diagnostic experience of whole-exome sequencing in adult patients. PMID:26633545
Clinical application of whole-exome sequencing across clinical indications. PMID:26633542
Lynx: a knowledge base and an analytical workbench for integrative medicine. PMID:26590263
Next-generation diagnostics and disease-gene discovery with the Exomiser. PMID:26562621
Computational evaluation of exome sequence data using human and model organism phenotypes improves diagnostic efficiency. PMID:26562225
Human genotype-phenotype databases: aims, challenges and opportunities. PMID:26553330
Umbilical cord gene expression reveals the molecular architecture of the fetal inflammatory response in extremely preterm newborns. PMID:26539667
MouseNet v2: a database of gene networks for studying the laboratory mouse and eight other model vertebrates. PMID:26527726
DIDA: A curated and annotated digenic diseases database. PMID:26481352
Rare disease diagnosis: A review of web search, social media and large-scale data-mining approaches. PMID:26442199
Prioritizing Clinically Relevant Copy Number Variation from Genetic Interactions and Gene Function Data. PMID:26437450
Discovery of four recessive developmental disorders using probabilistic genotype and phenotype matching among 4,125 families. PMID:26437029
Genome-Wide Detection and Analysis of Multifunctional Genes. PMID:26436655
The digital revolution in phenotyping. PMID:26420780
DIVAS: a centralized genetic variant repository representing 150,000 individuals from multiple disease cohorts. PMID:26363178
Applications of comparative evolution to human disease genetics. PMID:26338499
Adverse Drug Events-based Tumor Stratification for Ovarian Cancer Patients Receiving Platinum Therapy. PMID:26306234
Axons to Exons: the Molecular Diagnosis of Rare Neurological Diseases by Next-Generation Sequencing. PMID:26289954
Exome analysis of a family with Wolff-Parkinson-White syndrome identifies a novel disease locus. PMID:26284702
OVA: integrating molecular and physical phenotype data from multiple biomedical domain ontologies with variant filtering for enhanced variant prioritization. PMID:26272982
Use of model organism and disease databases to support matchmaking for human disease gene discovery. PMID:26269093
Extending the coverage of phenotypes in SNOMED CT through post-coordination. PMID:26262161
The Matchmaker Exchange API: automating patient matching through the exchange of structured phenotypic and genotypic profiles. PMID:26255989
PhenomeCentral: a portal for phenotypic and genotypic matchmaking of patients with rare genetic diseases. PMID:26251998
Phenotype-driven strategies for exome prioritization of human Mendelian disease genes. PMID:26229552
GeneMatcher: a matching tool for connecting investigators with an interest in the same gene. PMID:26220891
Best behaviour? Ontologies and the formal description of animal behaviour. PMID:26215546
Innovative genomic collaboration using the GENESIS (GEM.app) platform. PMID:26173844
Allele, phenotype and disease data at Mouse Genome Informatics: improving access and analysis. PMID:26162703
Relationships between predicted moonlighting proteins, human diseases, and comorbidities from a network perspective. PMID:26157390
Precision Medicine for Continuing Phenotype Expansion of Human Genetic Diseases. PMID:26137492
The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease. PMID:26119816
Using text mining techniques to extract phenotypic information from the PhenoCHF corpus. PMID:26099853
Cross-organism analysis using InterMine. PMID:26097192
The Disease Ontology: fostering interoperability between biological and clinical human disease-related data. PMID:26093607
Disease insights through cross-species phenotype comparisons. PMID:26092691
Analysis of the human diseasome using phenotype similarity between common, genetic, and infectious diseases. PMID:26051359
PANDA: pathway and annotation explorer for visualizing and interpreting gene-centric data. PMID:26038725
Transcription factor p63 bookmarks and regulates dynamic enhancers during epidermal differentiation. PMID:26034101
Adverse Drug Event-based Stratification of Tumor Mutations: A Case Study of Breast Cancer Patients Receiving Aromatase Inhibitors. PMID:25954427
Human phenotype ontology annotation and cluster analysis to unravel genetic defects in 707 cases with unexplained bleeding and platelet disorders. PMID:25949529
Galahad: a web server for drug effect analysis from gene expression. PMID:25940630
Linking gene expression to phenotypes via pathway information. PMID:25901272
DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes. PMID:25877637
GeneTIER: prioritization of candidate disease genes using tissue-specific gene expression profiles. PMID:25861967
Disease gene prioritization using network and feature. PMID:25844670
Ranking adverse drug reactions with crowdsourcing. PMID:25800813
Supporting the annotation of chronic obstructive pulmonary disease (COPD) phenotypes with text mining workflows. PMID:25789153
Performance of case-control rare copy number variation annotation in classification of autism. PMID:25783485
Gene networks underlying convergent and pleiotropic phenotypes in a large and systematically-phenotyped cohort with heterogeneous developmental disorders. PMID:25781962
An ontology approach to comparative phenomics in plants. PMID:25774204
Automatic concept recognition using the human phenotype ontology reference and test suite corpora. PMID:25725061
Integrative analysis of 111 reference human epigenomes. PMID:25693563
New tools for Mendelian disease gene identification: PhenoDB variant analysis module; and GeneMatcher, a web-based tool for linking investigators with an interest in the same gene. PMID:25684268
HPOSim: an R package for phenotypic similarity measure and enrichment analysis based on the human phenotype ontology. PMID:25664462
Whole-genome sequencing of quartet families with autism spectrum disorder. PMID:25621899
Phenomics research on coronary heart disease based on human phenotype ontology. PMID:25610858
Next generation phenotyping using the unified medical language system. PMID:25601137
Symptom-driven idiopathic disease gene identification. PMID:25590976
Finding our way through phenotypes. PMID:25562316
Mitochondrial Disease Sequence Data Resource (MSeqDR): a global grass-roots consortium to facilitate deposition, curation, annotation, and integrated analysis of genomic data for the mitochondrial disease clinical and research communities. PMID:25542617
Genomic data sharing for translational research and diagnostics. PMID:25473437
FLAGS, frequently mutated genes in public exomes. PMID:25466818
OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders. PMID:25428349
Delivery of a clinical genomics service. PMID:25383561
Defining disease phenotypes using national linked electronic health records: a case study of atrial fibrillation. PMID:25369203
dcGOR: an R package for analysing ontologies and protein domain annotations. PMID:25356683
Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data. PMID:25348409
Deletions of chromosomal regulatory boundaries are associated with congenital disease. PMID:25315429
Clinical interpretation of CNVs with cross-species phenotype data. PMID:25280750
Transcriptional diversity during lineage commitment of human blood progenitors. PMID:25258084
Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome. PMID:25186178
EHR Big Data Deep Phenotyping. Contribution of the IMIA Genomic Medicine Working Group. PMID:25123744
RD-Connect: an integrated platform connecting databases, registries, biobanks and clinical bioinformatics for rare disease research. PMID:25029978
Zebrafish models in translational research: tipping the scales toward advancements in human health. PMID:24973743
FORGE Canada Consortium: outcomes of a 2-year national rare-disease gene-discovery project. PMID:24906018
Automated semantic annotation of rare disease cases: a case study. PMID:24903515
MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network. PMID:24861622
Rare inherited kidney diseases: challenges, opportunities, and perspectives. PMID:24856029
Genetic variations and diseases in UniProtKB/Swiss-Prot: the ins and outs of expert manual curation. PMID:24848695
Commentary on Shimoyama et al. (2012): three ontologies to define phenotype measurement data. PMID:24795755
Phenotype ontologies and cross-species analysis for translational research. PMID:24699242
Thematic series on biomedical ontologies in JBMS: challenges and new directions. PMID:24602198
The Human Phenotype Ontology in 2017 PubMed citations: 316.

316 articles citing: The Human Phenotype Ontology in 2017

Enhancer promoter interactome and Mendelian randomization identify network of druggable vascular genes in coronary artery disease. PMID:35246263
GeneTerpret: a customizable multilayer approach to genomic variant prioritization and interpretation. PMID:35180879
Differential COVID-19 Symptoms Given Pandemic Locations, Time, and Comorbidities During the Early Pandemic. PMID:35155491
Cost Efficacy of Rapid Whole Genome Sequencing in the Pediatric Intensive Care Unit. PMID:35141181
Phenomic Analysis of Chronic Granulomatous Disease Reveals More Severe Integumentary Infections in X-Linked Compared With Autosomal Recessive Chronic Granulomatous Disease. PMID:35140711
Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases. PMID:35134823
ICEO, a biological ontology for representing and analyzing bacterial integrative and conjugative elements. PMID:35058462
Diagnosis of Genetic White Matter Disorders by Singleton Whole-Exome and Genome Sequencing Using Interactome-Driven Prioritization. PMID:35012964
Effects of Negation and Uncertainty Stratification on Text-Derived Patient Profile Similarity. PMID:34939069
Intellectual disability genomics: current state, pitfalls and future challenges. PMID:34930158
An Overview of Biomedical Ontologies for Pandemics and Infectious Diseases Representation. PMID:34868401
Quantitative dissection of multilocus pathogenic variation in an Egyptian infant with severe neurodevelopmental disorder resulting from multiple molecular diagnoses. PMID:34816580
PheneBank: a literature-based database of phenotypes. PMID:34788791
Gene4HL: An Integrated Genetic Database for Hearing Loss. PMID:34733322
Opportunities and Challenges for Machine Learning in Rare Diseases. PMID:34676229
Deep semi-supervised learning ensemble framework for classifying co-mentions of human proteins and phenotypes. PMID:34656098
Identifying digenic disease genes via machine learning in the Undiagnosed Diseases Network. PMID:34529933
A data-driven architecture using natural language processing to improve phenotyping efficiency and accelerate genetic diagnoses of rare disorders. PMID:34514437
Evaluating, Filtering and Clustering Genetic Disease Cohorts Based on Human Phenotype Ontology Data with Cohort Analyzer. PMID:34442375
Gut Microbiota and Neuroplasticity. PMID:34440854
A global map of associations between types of protein posttranslational modifications and human genetic diseases. PMID:34430807
X-CNV: genome-wide prediction of the pathogenicity of copy number variations. PMID:34407882
Novel phenotype and genotype spectrum of NARS2 and literature review of previous mutations. PMID:34374940
The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research. PMID:34367618
ACO2 clinicobiological dataset with extensive phenotype ontology annotation. PMID:34354088
Congenital anomalies and genetic disorders in neonates and infants: a single-center observational cohort study. PMID:34347148
DES-Tcell is a knowledgebase for exploring immunology-related literature. PMID:34253812
CDON gene contributes to pituitary stalk interruption syndrome associated with unilateral facial and abducens nerve palsy. PMID:34235642
Genotype-Phenotype Correlations in Neurofibromatosis and Their Potential Clinical Use. PMID:34230207
Visual comprehension and orientation into the COVID-19 CIDO ontology. PMID:34224898
Genotype-by-environment interactions for reproduction, body composition, and growth traits in maternal-line pigs based on single-step genomic reaction norms. PMID:34139991
Defining Phenotypes from Clinical Data to Drive Genomic Research. PMID:34109303
Diagnostic yield of exome sequencing in myopathies: Experience of a Slovenian tertiary centre. PMID:34106991
Whole-Genome Sequencing of Common Salivary Gland Carcinomas: Subtype-Restricted and Shared Genetic Alterations. PMID:34011559
Finding commonalities in rare diseases through the undiagnosed diseases network. PMID:34009343
Semantic standards of external exposome data. PMID:33901445
The VRNetzer platform enables interactive network analysis in Virtual Reality. PMID:33893283
Rapid whole genome sequencing impacts care and resource utilization in infants with congenital heart disease. PMID:33888711
GPCards: An integrated database of genotype-phenotype correlations in human genetic diseases. PMID:33868597
Phenotyping the Spectrum of Traumatic Brain Injury: A Review and Pathway to Standardization. PMID:33858210
Improved characterisation of clinical text through ontology-based vocabulary expansion. PMID:33845909
Treatable inherited metabolic disorders causing intellectual disability: 2021 review and digital app. PMID:33845862
Primary immunodeficiency-related genes in neonatal intensive care unit patients with various genetic immune abnormalities: a multicentre study in China. PMID:33777394
Science for the Next Century: Deep Phenotyping. PMID:33749358
An Early Stage Researcher's Primer on Systems Medicine Terminology. PMID:33659919
Rationale and design of the Kidney Precision Medicine Project. PMID:33637194
The similarity of inherited diseases (I): clinical similarity within the phenotypic series. PMID:33622316
Converting disease maps into heavyweight ontologies: general methodology and application to Alzheimer's disease. PMID:33590873
A Case of UDP-Galactose 4'-Epimerase Deficiency Associated with Dyshematopoiesis and Atrioventricular Valve Malformations: An Exceptional Clinical Phenotype Explained by Altered N-Glycosylation with Relative Preservation of the Leloir Pathway. PMID:33510604
A cross-platform approach identifies genetic regulators of human metabolism and health. PMID:33414548
Usher syndrome and Nebulin-associated myopathy in a single patient due to variants in MYO7A and NEB. PMID:33363762
Ontological representation, classification and data-driven computing of phenotypes. PMID:33349245
A Comprehensive Assessment of Co-occurring Birth Defects among Infants with Non-Syndromic Anophthalmia or Microphthalmia. PMID:33345678
Integrating comprehensive functional annotations to boost power and accuracy in gene-based association analysis. PMID:33320851
Ambiguity in medical concept normalization: An analysis of types and coverage in electronic health record datasets. PMID:33319905
The Human Phenotype Ontology in 2021. PMID:33264411
A hybrid approach toward biomedical relation extraction training corpora: combining distant supervision with crowdsourcing. PMID:33258966
What Can Machine Learning Approaches in Genomics Tell Us about the Molecular Basis of Amyotrophic Lateral Sclerosis? PMID:33256133
Application of Next-Generation Sequencing for Genetic Diagnosis in Neonatal Intensive Care Units: Results of a Multicenter Study in China. PMID:33240318
Transforming the study of organisms: Phenomic data models and knowledge bases. PMID:33232313
Developmental constraint shaped genome evolution and erythrocyte loss in Antarctic fishes following paleoclimate change. PMID:33108368
Finding disease modules for cancer and COVID-19 in gene co-expression networks with the Core&Peel method. PMID:33077837
Integration of anatomy ontology data with protein-protein interaction networks improves the candidate gene prediction accuracy for anatomical entities. PMID:33028186
Disease trajectory browser for exploring temporal, population-wide disease progression patterns in 7.2 million Danish patients. PMID:33009368
The similarity of inherited diseases (II): clinical and biological similarity between the phenotypic series. PMID:32972400
Developments in evidence creation for treatments of inborn errors of metabolism. PMID:32944978
The Application of Next-Generation Sequencing (NGS) in Neonatal-Onset Urea Cycle Disorders (UCDs): Clinical Course, Metabolomic Profiling, and Genetic Findings in Nine Chinese Hyperammonemia Patients. PMID:32934962
Long non-coding RNA MIR4300HG polymorphisms are associated with postoperative nausea and vomiting: a genome-wide association study. PMID:32928300
SCALEUS-FD: A FAIR Data Tool for Biomedical Applications. PMID:32908882
Semantic Similarity Analysis Reveals Robust Gene-Disease Relationships in Developmental and Epileptic Encephalopathies. PMID:32853554
Interpretable Clinical Genomics with a Likelihood Ratio Paradigm. PMID:32755546
Hybrid phenotype mining method for investigating off-target protein and underlying side effects of anti-tumor immunotherapy. PMID:32646421
Genetic background of ataxia in children younger than 5 years in Finland. PMID:32637629
SEMA3A and IGSF10 Are Novel Contributors to Combined Pituitary Hormone Deficiency (CPHD). PMID:32612575
Quantitative analysis of proteins which are members of the same protein complex but cause locus heterogeneity in disease. PMID:32591566
DDIEM: drug database for inborn errors of metabolism. PMID:32527280
Digenic inheritance of subclinical variants in Noonan Syndrome patients: an alternative pathogenic model? PMID:32514133
Aggregation and analysis of indication-symptom relationships for drugs approved in the USA. PMID:32495081
Network pharmacology to dissect the mechanisms of Yinlai Decoction for pneumonia. PMID:32493296
The undiagnosed diseases program: Approach to diagnosis. PMID:32477883
Spectrum of Germline BRCA1 and BRCA2 Variants Identified in 2351 Ovarian and Breast Cancer Patients Referring to a Reference Cancer Hospital of Rome. PMID:32438681
Rare Genetic Diseases: Nature's Experiments on Human Development. PMID:32422592
Mantis-ml: Disease-Agnostic Gene Prioritization from High-Throughput Genomic Screens by Stochastic Semi-supervised Learning. PMID:32386536
Disease-associated mosaic variation in clinical exome sequencing: a two-year pediatric tertiary care experience. PMID:32371413
Genotype-phenotype correlations of Berardinelli-Seip congenital lipodystrophy and novel candidate genes prediction. PMID:32349771
An Improved Phenotype-Driven Tool for Rare Mendelian Variant Prioritization: Benchmarking Exomiser on Real Patient Whole-Exome Data. PMID:32340307
The phenotype-driven computational analysis yields clinical diagnosis for patients with atypical manifestations of known intellectual disability syndromes. PMID:32337850
PRIORI-T: A tool for rare disease gene prioritization using MEDLINE. PMID:32315351
FHIR OWL: Transforming OWL ontologies into FHIR terminology resources. PMID:32308861
DES-ROD: Exploring Literature to Develop New Links between RNA Oxidation and Human Diseases. PMID:32308806
Phenogenon: Gene to phenotype associations for rare genetic diseases. PMID:32271766
Rare diseases 2030: how augmented AI will support diagnosis and treatment of rare diseases in the future. PMID:32209541
Wikidata as a knowledge graph for the life sciences. PMID:32180547
ncRPheno: a comprehensive database platform for identification and validation of disease related noncoding RNAs. PMID:32122231
DISNET: a framework for extracting phenotypic disease information from public sources. PMID:32110491
Machine Learning and Bioinformatics Models to Identify Pathways that Mediate Influences of Welding Fumes on Cancer Progression. PMID:32066756
Five new cases of syndromic intellectual disability due to KAT6A mutations: widening the molecular and clinical spectrum. PMID:32041641
Organizing genome engineering for the gigabase scale. PMID:32019919
Significantly different clinical phenotypes associated with mutations in synthesis and transamidase+remodeling glycosylphosphatidylinositol (GPI)-anchor biosynthesis genes. PMID:32019583
Annotating and detecting phenotypic information for chronic obstructive pulmonary disease. PMID:31984360
Study of the Gastrointestinal Heat Retention Syndrome in Children: From Diagnostic Model to Biological Basis. PMID:31929814
Mechanisms of tissue and cell-type specificity in heritable traits and diseases. PMID:31913361
Edematous severe acute malnutrition is characterized by hypomethylation of DNA. PMID:31857576
MGeND: an integrated database for Japanese clinical and genomic information. PMID:31839973
Formal axioms in biomedical ontologies improve analysis and interpretation of associated data. PMID:31821406
Hypothesis: determining phenotypic specificity facilitates understanding of pathophysiology in rare genetic disorders. PMID:31804708
Cardioinformatics: the nexus of bioinformatics and precision cardiology. PMID:31802103
Prioritization of genes driving congenital phenotypes of patients with de novo genomic structural variants. PMID:31801603
Proposed minimum information guideline for kidney disease-research and clinical data reporting: a cross-sectional study. PMID:31772086
The Sickle Cell Disease Ontology: enabling universal sickle cell-based knowledge representation. PMID:31769834
The Hearing Impairment Ontology: A Tool for Unifying Hearing Impairment Knowledge to Enhance Collaborative Research. PMID:31766582
I3: A Self-organising Learning Workflow for Intuitive Integrative Interpretation of Complex Genetic Data. PMID:31765831
Mapping the perturbome network of cellular perturbations. PMID:31723137
Rapid Whole Genome Sequencing and Fulfilling the Promise of Precision Pediatric Critical Care. PMID:31688677
PPR-SSM: personalized PageRank and semantic similarity measures for entity linking. PMID:31664891
Missense variants in TAF1 and developmental phenotypes: challenges of determining pathogenicity. PMID:31646703
Gene4Denovo: an integrated database and analytic platform for de novo mutations in humans. PMID:31642496
Biological Network Approaches and Applications in Rare Disease Studies. PMID:31614842
Bradykinin-Mediated Angioedema: An Update of the Genetic Causes and the Impact of Genomics. PMID:31611908
Comparison of Causative Variant Prioritization Tools Using Next-generation Sequencing Data in Japanese Patients with Mendelian Disorders. PMID:31582890
A framework for the investigation of rare genetic disorders in neuropsychiatry. PMID:31548702
Using MARRVEL v1.2 for Bioinformatics Analysis of Human Genes and Variant Pathogenicity. PMID:31524990
OPA1: 516 unique variants and 831 patients registered in an updated centralized Variome database. PMID:31500643
A Survey of Gene Prioritization Tools for Mendelian and Complex Human Diseases. PMID:31494632
Encoding Clinical Data with the Human Phenotype Ontology for Computational Differential Diagnostics. PMID:31479590
Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information. PMID:31475990
Enabling Global Clinical Collaborations on Identifiable Patient Data: The Minerva Initiative. PMID:31417602
Genomic medicine for undiagnosed diseases. PMID:31395441
Mapping the knowledge structure and trends of epilepsy genetics over the past decade: A co-word analysis based on medical subject headings terms. PMID:31393404
RNA sequencing profiling of the retina in C57BL/6J and DBA/2J mice: Enhancing the retinal microarray data sets from GeneNetwork. PMID:31354228
Fetal phenotypes emerge as genetic technologies become robust. PMID:31330568
PhenPath: a tool for characterizing biological functions underlying different phenotypes. PMID:31307376
A Novel Intelligent Scan Assistant System for Early Pregnancy Diagnosis by Ultrasound: Clinical Decision Support System Evaluation Study. PMID:31271152
A genetics-led approach defines the drug target landscape of 30 immune-related traits. PMID:31253980
Improving the diagnostic yield of exome- sequencing by predicting gene-phenotype associations using large-scale gene expression analysis. PMID:31253775
Literature-Based Enrichment Insights into Redox Control of Vascular Biology. PMID:31223421
Clinical presentation and genetic profiles of Chinese patients with velocardiofacial syndrome in a large referral centre. PMID:31204702
Historical contingency shapes adaptive radiation in Antarctic fishes. PMID:31182814
Ontology-Based Interactive Visualization of Patient-Generated Research Questions. PMID:31167249
Identification of rare-disease genes using blood transcriptome sequencing and large control cohorts. PMID:31160820
Semantic integration of clinical laboratory tests from electronic health records for deep phenotyping and biomarker discovery. PMID:31119199
MutationDistiller: user-driven identification of pathogenic DNA variants. PMID:31106342
A Recurrent Missense Variant in AP2M1 Impairs Clathrin-Mediated Endocytosis and Causes Developmental and Epileptic Encephalopathy. PMID:31104773
Identifying Clinical Terms in Medical Text Using Ontology-Guided Machine Learning. PMID:31094361
Elevated CCL19/CCR7 Expression During the Disease Process of Primary Sjögren's Syndrome. PMID:31068931
Diagnostic high-throughput sequencing of 2396 patients with bleeding, thrombotic, and platelet disorders. PMID:31064749
Exome Sequencing in Children. PMID:31056085
VarWatch-A stand-alone software tool for variant matching. PMID:31022234
De novo Mutations From Whole Exome Sequencing in Neurodevelopmental and Psychiatric Disorders: From Discovery to Application. PMID:31001316
Glutaminase Deficiency Caused by Short Tandem Repeat Expansion in GLS. PMID:30970188
A toolkit for genetics providers in follow-up of patients with non-diagnostic exome sequencing. PMID:30964584
Phenotypes associated with genes encoding drug targets are predictive of clinical trial side effects. PMID:30952858
Evolution and Comprehensive Analysis of DNaseI Hypersensitive Sites in Regulatory Regions of Primate Brain-Related Genes. PMID:30930929
Opportunities and Challenges for Molecular Understanding of Ciliopathies-The 100,000 Genomes Project. PMID:30915099
Can a decision support system accelerate rare disease diagnosis? Evaluating the potential impact of Ada DX in a retrospective study. PMID:30898118
Prioritization of genes involved in endothelial cell apoptosis by their implication in lymphedema using an analysis of associative gene networks with ANDSystem. PMID:30871556
GenCoNet - A Graph Database for the Analysis of Comorbidities by Gene Networks. PMID:30864352
SNPs2ChIP: Latent Factors of ChIP-seq to infer functions of non-coding SNPs. PMID:30864321
Xenbase: Facilitating the Use of Xenopus to Model Human Disease. PMID:30863320
Whole genome sequencing reveals that genetic conditions are frequent in intensively ill children. PMID:30847515
How Sustainable are Biomedical Ontologies? PMID:30815087
ClinTAD: a tool for copy number variant interpretation in the context of topologically associated domains. PMID:30765865
A semiautomated whole-exome sequencing workflow leads to increased diagnostic yield and identification of novel candidate variants. PMID:30755392
The mutational and phenotypic spectrum of TUBA1A-associated tubulinopathy. PMID:30744660
Functional characterization of a novel CSF1R mutation causing hereditary diffuse leukoencephalopathy with spheroids. PMID:30729751
Apollo: Democratizing genome annotation. PMID:30726205
Developing a genomics rotation: Practical training around variant interpretation for genetic counseling students. PMID:30706981
Data Lakes, Clouds, and Commons: A Review of Platforms for Analyzing and Sharing Genomic Data. PMID:30691868
Xrare: a machine learning method jointly modeling phenotypes and genetic evidence for rare disease diagnosis. PMID:30675030
The utility of phenomics in diagnosis of inherited metabolic disorders. PMID:30651242
Rapid and accurate interpretation of clinical exomes using Phenoxome: a computational phenotype-driven approach. PMID:30626929
An ontological foundation for ocular phenotypes and rare eye diseases. PMID:30626441
Integrating ontologies of human diseases, phenotypes, and radiological diagnosis. PMID:30624645
BO-LSTM: classifying relations via long short-term memory networks along biomedical ontologies. PMID:30616557
Artificial Intelligence and Integrated Genotype⁻Phenotype Identification. PMID:30597900
Integrative network and brain expression analysis reveals mechanistic modules in ataxia. PMID:30591515
Pathogenicity and selective constraint on variation near splice sites. PMID:30587507
Annotation of phenotypes using ontologies: a gold standard for the training and evaluation of natural language processing systems. PMID:30576485
Estimating the burden and economic impact of pediatric genetic disease. PMID:30568310
Early-onset inflammatory bowel disease as a model disease to identify key regulators of immune homeostasis mechanisms. PMID:30565237
Diagnosing rare diseases after the exome. PMID:30559314
Concomitant diagnosis of immune deficiency and Pseudomonas sepsis in a 19 month old with ecthyma gangrenosum by host whole-genome sequencing. PMID:30559311
Integrating molecular networks with genetic variant interpretation for precision medicine. PMID:30548534
Development and user evaluation of a rare disease gene prioritization workflow based on cognitive ergonomics. PMID:30535356
Modifier Ontologies for frequency, certainty, degree, and coverage phenotype modifier. PMID:30532623
The effect of copy number variations in chromosome 16p on body weight in patients with intellectual disability. PMID:30518945
ClinPhen extracts and prioritizes patient phenotypes directly from medical records to expedite genetic disease diagnosis. PMID:30514889
A nomenclature and classification for the congenital myasthenic syndromes: preparing for FAIR data in the genomic era. PMID:30477555
Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. PMID:30476213
Open Targets Platform: new developments and updates two years on. PMID:30462303
Assembly of a parts list of the human mitotic cell cycle machinery. PMID:30452682
OMIM.org: leveraging knowledge across phenotype-gene relationships. PMID:30445645
Semantic Disease Gene Embeddings (SmuDGE): phenotype-based disease gene prioritization without phenotypes. PMID:30423077
Ontology-based validation and identification of regulatory phenotypes. PMID:30423068
Widespread Genotype-Phenotype Correlations in Intellectual Disability. PMID:30420816
HumanNet v2: human gene networks for disease research. PMID:30418591
Human Disease Ontology 2018 update: classification, content and workflow expansion. PMID:30407550
Novel Factor XIII variant identified through whole-genome sequencing in a child with intracranial hemorrhage. PMID:30404926
From scientific discovery to treatments for rare diseases - the view from the National Center for Advancing Translational Sciences - Office of Rare Diseases Research. PMID:30400963
Resolving "orphaned" non-specific structures using machine learning and natural language processing methods. PMID:30393454
Precision global health and comorbidity: a population-based study of 16 357 people in rural Uganda. PMID:30381343
SymMap: an integrative database of traditional Chinese medicine enhanced by symptom mapping. PMID:30380087
VarSome: the human genomic variant search engine. PMID:30376034
Genotype and phenotype variability in Sjögren-Larsson syndrome. PMID:30372562
Heterogeneous network embedding for identifying symptom candidate genes. PMID:30357378
Rationalizing Secondary Pharmacology Screening Using Human Genetic and Pharmacological Evidence. PMID:30346593
AutismKB 2.0: a knowledgebase for the genetic evidence of autism spectrum disorder. PMID:30339214
The value of genomic variant ClinVar submissions from clinical providers: Beyond the addition of novel variants. PMID:30311381
The ClinGen Epilepsy Gene Curation Expert Panel-Bridging the divide between clinical domain knowledge and formal gene curation criteria. PMID:30311377
ClinGen's GenomeConnect registry enables patient-centered data sharing. PMID:30311371
Classification, Ontology, and Precision Medicine. PMID:30304648
The Italian neuromuscular registry: a coordinated platform where patient organizations and clinicians collaborate for data collection and multiple usage. PMID:30286784
OligoPVP: Phenotype-driven analysis of individual genomic information to prioritize oligogenic disease variants. PMID:30279426
Identifying High-Priority Proteins Across the Human Diseasome Using Semantic Similarity. PMID:30256117
Pathway networks generated from human disease phenome. PMID:30255817
Meeting Patients' Right to the Correct Diagnosis: Ongoing International Initiatives on Undiagnosed Rare Diseases and Ethical and Social Issues. PMID:30248891
matchbox: An open-source tool for patient matching via the Matchmaker Exchange. PMID:30240502
Identifying core biological processes distinguishing human eye tissues with precise systems-level gene expression analyses and weighted correlation networks. PMID:30239781
Comprehensive screening shows that mutations in the known syndromic genes are rare in infants presenting with hyperinsulinaemic hypoglycaemia. PMID:30238501
Model organism data evolving in support of translational medicine. PMID:30224793
DES-Mutation: System for Exploring Links of Mutations and Diseases. PMID:30190574
PubCaseFinder: A Case-Report-Based, Phenotype-Driven Differential-Diagnosis System for Rare Diseases. PMID:30173820
Setting the stage for a role of the postsynaptic proteome in inherited neurometabolic disorders. PMID:30132229
An integrated clinical program and crowdsourcing strategy for genomic sequencing and Mendelian disease gene discovery. PMID:30131872
SpainUDP: The Spanish Undiagnosed Rare Diseases Program. PMID:30110963
SYT1-associated neurodevelopmental disorder: a case series. PMID:30107533
Computational resources associating diseases with genotypes, phenotypes and exposures. PMID:30102366
The International Mouse Phenotyping Consortium (IMPC): a functional catalogue of the mammalian genome that informs conservation. PMID:30100824
HPO2GO: prediction of human phenotype ontology term associations for proteins using cross ontology annotation co-occurrences. PMID:30083448
Cardiovascular Precision Medicine in the Genomics Era. PMID:30062216
IRF2BPL Is Associated with Neurological Phenotypes. PMID:30057031
Clinical genome sequencing in an unbiased pediatric cohort. PMID:30008475
IDPpi: Protein-Protein Interaction Analyses of Human Intrinsically Disordered Proteins. PMID:30002402
CDG: An Online Server for Detecting Biologically Closest Disease-Causing Genes and its Application to Primary Immunodeficiency. PMID:29997612
[From symptom to syndrome using modern software support]. PMID:29995249
Phenotype-driven gene prioritization for rare diseases using graph convolution on heterogeneous networks. PMID:29980210
Clinical and genetic analyses of a Dutch cohort of 40 patients with a nephronophthisis-related ciliopathy. PMID:29974258
Deep Phenotyping on Electronic Health Records Facilitates Genetic Diagnosis by Clinical Exomes. PMID:29961570
Phenotype-loci associations in networks of patients with rare disorders: application to assist in the diagnosis of novel clinical cases. PMID:29946186
Whole-genome sequencing reveals a recurrent missense mutation in the Connexin 46 (GJA3) gene causing autosomal-dominant lamellar cataract. PMID:29934635
Recommendations on Collecting and Storing Samples for Genetic Studies in Hearing and Tinnitus Research. PMID:29889665
GNOMICS: A one-stop shop for biomedical and genomic data. PMID:29888054
Whole Exome Sequencing of Patients from Multicase Families with Systemic Lupus Erythematosus Identifies Multiple Rare Variants. PMID:29884787
ClinVar Miner: Demonstrating utility of a Web-based tool for viewing and filtering ClinVar data. PMID:29790234
A new method to measure the semantic similarity from query phenotypic abnormalities to diseases based on the human phenotype ontology. PMID:29745853
Emerging Role of Precision Medicine in Cardiovascular Disease. PMID:29700074
Improved ontology-based similarity calculations using a study-wise annotation model. PMID:29688377
Biocuration: Distilling data into knowledge. PMID:29659566
Plain-language medical vocabulary for precision diagnosis. PMID:29632381
High-throughput mouse phenomics for characterizing mammalian gene function. PMID:29626206
Delineating the psychiatric and behavioral phenotype of recurrent 2q13 deletions and duplications. PMID:29603867
The rendering of human phenotype and rare diseases in ICD-11. PMID:29600497
Disease Ontology: improving and unifying disease annotations across species. PMID:29590633
GENEASE: real time bioinformatics tool for multi-omics and disease ontology exploration, analysis and visualization. PMID:29590301
A genomics approach reveals insights into the importance of gene losses for mammalian adaptations. PMID:29572503
De novo mutations in regulatory elements in neurodevelopmental disorders. PMID:29562236
The case for early use of rapid whole-genome sequencing in management of critically ill infants: late diagnosis of Coffin-Siris syndrome in an infant with left congenital diaphragmatic hernia, congenital heart disease, and recurrent infections. PMID:29549119
A FAIR guide for data providers to maximise sharing of human genomic data. PMID:29543799
Accelerated Evolution in Distinctive Species Reveals Candidate Elements for Clinically Relevant Traits, Including Mutation and Cancer Resistance. PMID:29514101
RD-Connect, NeurOmics and EURenOmics: collaborative European initiative for rare diseases. PMID:29487416
A Human Stem Cell-Based System to Study the Role of TP63 Mutations in Ectodermal Dysplasias. PMID:29481901
Mutation in an alternative transcript of CDKL5 in a boy with early-onset seizures. PMID:29444904
Points to consider for sharing variant-level information from clinical genetic testing with ClinVar. PMID:29437798
Rapid whole-genome sequencing identifies a novel AIRE variant associated with autoimmune polyendocrine syndrome type 1. PMID:29437776
Integrated Modules Analysis to Explore the Molecular Mechanisms of Phlegm-Stasis Cementation Syndrome with Ischemic Heart Disease. PMID:29403392
Rare Disease Mechanisms Identified by Genealogical Proteomics of Copper Homeostasis Mutant Pedigrees. PMID:29397366
The RD-Connect Registry & Biobank Finder: a tool for sharing aggregated data and metadata among rare disease researchers. PMID:29396563
GenIO: a phenotype-genotype analysis web server for clinical genomics of rare diseases. PMID:29374474
Systematic identification of latent disease-gene associations from PubMed articles. PMID:29373609
Scuba: scalable kernel-based gene prioritization. PMID:29370760
Text-based phenotypic profiles incorporating biochemical phenotypes of inborn errors of metabolism improve phenomics-based diagnosis. PMID:29340838
Comparison, alignment, and synchronization of cell line information between CLO and EFO. PMID:29322915
Update on 13 Syndromes Affecting Craniofacial and Dental Structures. PMID:29311971
The retina/RPE proteome in chick myopia and hyperopia models: Commonalities with inherited and age-related ocular pathologies. PMID:29259393
Fair data for next-generation management of multiple sclerosis. PMID:29254434
Identifying Human Phenotype Terms by Combining Machine Learning and Validation Rules. PMID:29250549
A novel missense mutation in HSF4 causes autosomal-dominant congenital lamellar cataract in a British family. PMID:29243736
Primary Ovarian Insufficiency and Azoospermia in Carriers of a Homozygous PSMC3IP Stop Gain Mutation. PMID:29240891
Fundamentals of Precision Medicine. PMID:29227115
An ontology-aware integration of clinical models, terminologies and guidelines: an exploratory study of the Scale for the Assessment and Rating of Ataxia (SARA). PMID:29207981
Matching disease and phenotype ontologies in the ontology alignment evaluation initiative. PMID:29197409
The European Bioinformatics Institute in 2017: data coordination and integration. PMID:29186510
Molecular Autopsy for Sudden Death in the Young: Is Data Aggregation the Key? PMID:29181379
ClinVar: improving access to variant interpretations and supporting evidence. PMID:29165669
The International Rare Diseases Research Consortium: Policies and Guidelines to maximize impact. PMID:29158551
PedAM: a database for Pediatric Disease Annotation and Medicine. PMID:29126123
VarCards: an integrated genetic and clinical database for coding variants in the human genome. PMID:29112736
eRAM: encyclopedia of rare disease annotations for precision medicine. PMID:29106618
Mouse Genome Database (MGD)-2018: knowledgebase for the laboratory mouse. PMID:29092072
Whole exome sequencing in 342 congenital cardiac left sided lesion cases reveals extensive genetic heterogeneity and complex inheritance patterns. PMID:29089047
A Review of Recent Advances in Translational Bioinformatics: Bridges from Biology to Medicine. PMID:29063562
Prediction of Human Phenotype Ontology terms by means of hierarchical ensemble methods. PMID:29025394
Revisiting biomarker discovery by plasma proteomics. PMID:28951502
Preaxial polydactyly of the foot. PMID:28946786
BIOSSES: a semantic sentence similarity estimation system for the biomedical domain. PMID:28881973
Rapid whole-genome sequencing identifies a novel GABRA1 variant associated with West syndrome. PMID:28864462
Mouse Genome Informatics (MGI) Resource: Genetic, Genomic, and Biological Knowledgebase for the Laboratory Mouse. PMID:28838066
Inferred inheritance of MorbidMap genes without OMIM clinical synopsis. PMID:28837159
Settling the score: variant prioritization and Mendelian disease. PMID:28804138
Future of Rare Diseases Research 2017-2027: An IRDiRC Perspective. PMID:28796445
Genomic analysis of an infant with intractable diarrhea and dilated cardiomyopathy. PMID:28701297
Systematic screening for skin, hair, and nail abnormalities in a large-scale knockout mouse program. PMID:28700664
"Matching" consent to purpose: The example of the Matchmaker Exchange. PMID:28699299
Disease model discovery from 3,328 gene knockouts by The International Mouse Phenotyping Consortium. PMID:28650483
Defining Disease, Diagnosis, and Translational Medicine within a Homeostatic Perturbation Paradigm: The National Institutes of Health Undiagnosed Diseases Program Experience. PMID:28603714
Rapid whole-genome sequencing identifies a novel homozygous NPC1 variant associated with Niemann-Pick type C1 disease in a 7-week-old male with cholestasis. PMID:28550066
Increased Survival and Partly Preserved Cognition in a Patient With ACO2-Related Disease Secondary to a Novel Variant. PMID:28545339
HGVA: the Human Genome Variation Archive. PMID:28535294
A pipeline combining multiple strategies for prioritizing heterozygous variants for the identification of candidate genes in exome datasets. PMID:28532469
Recent advances in predicting gene-disease associations. PMID:28529714
International Cooperation to Enable the Diagnosis of All Rare Genetic Diseases. PMID:28475856
Integrated network analysis reveals potentially novel molecular mechanisms and therapeutic targets of refractory epilepsies. PMID:28388656
The anatomy of phenotype ontologies: principles, properties and applications. PMID:28387809
Resequencing at scale in neurodevelopmental disorders. PMID:28358133
Whole genome sequencing of one complex pedigree illustrates challenges with genomic medicine. PMID:28228131
The Impact of Next-Generation Sequencing on the Diagnosis and Treatment of Epilepsy in Paediatric Patients. PMID:28197949
Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources PubMed citations: 208.

208 articles citing: Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources

Predicting genes from phenotypes using human phenotype ontology (HPO) terms. PMID:35357580
Functional Enrichment Analysis of Regulatory Elements. PMID:35327392
Towards more patient friendly clinical notes through language models and ontologies. PMID:35308976
A Data-Driven Medical Decision Framework for Associating Adverse Drug Events with Drug-Drug Interaction Mechanisms. PMID:35281526
A guide for the diagnosis of rare and undiagnosed disease: beyond the exome. PMID:35220969
Evolutionary rewiring of regulatory networks contributes to phenotypic differences between human and mouse orthologous genes. PMID:35137181
PhenoApt leverages clinical expertise to prioritize candidate genes via machine learning. PMID:35063063
ClinGen Variant Curation Interface: a variant classification platform for the application of evidence criteria from ACMG/AMP guidelines. PMID:35039090
Mitochondrial disease manifestations in relation to transcriptome location and function. PMID:34972656
DeepSVP: Integration of genotype and phenotype for structural variant prioritization using deep learning. PMID:34951628
SVInterpreter: A Comprehensive Topologically Associated Domain-Based Clinical Outcome Prediction Tool for Balanced and Unbalanced Structural Variants. PMID:34925449
Dimensional reduction of phenotypes from 53 000 mouse models reveals a diverse landscape of gene function. PMID:34870209
Characterizing Long COVID: Deep Phenotype of a Complex Condition. PMID:34839263
The Aliment to Bodily Condition knowledgebase (ABCkb): a database connecting plants and human health. PMID:34838100
The Immune Deficiency and Dysregulation Activity (IDDA2.1 'Kaleidoscope') Score and Other Clinical Measures in Inborn Errors of Immunity. PMID:34797428
HFIP: an integrated multi-omics data and knowledge platform for the precision medicine of heart failure. PMID:34791105
Phenotype-tissue expression and exploration (PTEE) resource facilitates the choice of tissue for RNA-seq-based clinical genetics studies. PMID:34743696
Mouse Genome Informatics (MGI): latest news from MGD and GXD. PMID:34698891
Prenatal phenotype of PNKP-related primary microcephaly associated with variants affecting both the FHA and phosphatase domain. PMID:34697416
Text Mining for Building Biomedical Networks Using Cancer as a Case Study. PMID:34680062
Deep semi-supervised learning ensemble framework for classifying co-mentions of human proteins and phenotypes. PMID:34656098
Whole-exome sequencing identified first homozygous frameshift variant in the COLEC10 gene in an Iranian patient causing 3MC syndrome type 3. PMID:34636477
A meta-analysis of prognostic biomarkers in neonatal retinal hemorrhage. PMID:34623569
Identification of a Rare Case With Nagashima-Type Palmoplantar Keratoderma and 18q Deletion Syndrome via Exome Sequencing and Low-Coverage Whole-Genome Sequencing. PMID:34616427
Proposed criteria for nevoid basal cell carcinoma syndrome in children assessed using statistical optimization. PMID:34611197
Very Elevated IgE, Atopy, and Severe Infection: A Genomics-Based Diagnostic Approach to a Spectrum of Diseases. PMID:34603803
The phenotypic spectrum of KCNT1: a new family with variable epilepsy syndromes including mild focal epilepsy. PMID:34537872
Exome Sequencing of 5 Families with Severe Early-Onset Periodontitis. PMID:34515563
CADA: phenotype-driven gene prioritization based on a case-enriched knowledge graph. PMID:34514393
GRAND: a database of gene regulatory network models across human conditions. PMID:34508353
Utility of Gene Panels for the Diagnosis of Inborn Errors of Metabolism in a Metabolic Reference Center. PMID:34440436
A global map of associations between types of protein posttranslational modifications and human genetic diseases. PMID:34430807
Evaluating the performance of a clinical genome sequencing program for diagnosis of rare genetic disease, seen through the lens of craniosynostosis. PMID:34429528
MitoPhen database: a human phenotype ontology-based approach to identify mitochondrial DNA diseases. PMID:34428295
PhenoDB, GeneMatcher and VariantMatcher, tools for analysis and sharing of sequence data. PMID:34407837
Increased Cancer Prevalence in Peripartum Cardiomyopathy. PMID:34396183
Patients with PWS and related syndromes display differentially methylated regions involved in neurodevelopmental and nutritional trajectory. PMID:34389046
Diffusion enables integration of heterogeneous data and user-driven learning in a desktop knowledge-base. PMID:34379637
ACO2 clinicobiological dataset with extensive phenotype ontology annotation. PMID:34354088
Exploring the Impact of Cerebrovascular Disease and Major Depression on Non-diseased Human Tissue Transcriptomes. PMID:34349785
DTI-Voodoo: machine learning over interaction networks and ontology-based background knowledge predicts drug-target interactions. PMID:34320178
Dynamic changes in RNA-protein interactions and RNA secondary structure in mammalian erythropoiesis. PMID:34315813
Disease ontologies for knowledge graphs. PMID:34289807
A Biomedical Knowledge Graph System to Propose Mechanistic Hypotheses for Real-World Environmental Health Observations: Cohort Study and Informatics Application. PMID:34283031
Genetic testing in the diagnosis of chronic kidney disease: recommendations for clinical practice. PMID:34264297
A comprehensive review of integrative pharmacology-based investigation: A paradigm shift in traditional Chinese medicine. PMID:34221858
Development and application of the ocular immune-mediated inflammatory diseases ontology enhanced with synonyms from online patient support forum conversation. PMID:34139439
Transcriptomic analyses of gastrulation-stage mouse embryos with differential susceptibility to alcohol. PMID:34137816
Evaluating the clinical utility of early exome sequencing in diverse pediatric outpatient populations in the North Carolina Clinical Genomic Evaluation of Next-generation Exome Sequencing (NCGENES) 2 study: a randomized controlled trial. PMID:34127041
GenomeDiver: a platform for phenotype-guided medical genomic diagnosis. PMID:34113009
Genomic insights into body size evolution in Carnivora support Peto's paradox. PMID:34107880
Cruxome: a powerful tool for annotating, interpreting and reporting genetic variants. PMID:34082700
Solving patients with rare diseases through programmatic reanalysis of genome-phenome data. PMID:34075210
TSPEAR variants are primarily associated with ectodermal dysplasia and tooth agenesis but not hearing loss: A novel cohort study. PMID:34042254
PhenCards: a data resource linking human phenotype information to biomedical knowledge. PMID:34034817
GWENA: gene co-expression networks analysis and extended modules characterization in a single Bioconductor package. PMID:34034647
Mapping OMIM Disease-Related Variations on Protein Domains Reveals an Association Among Variation Type, Pfam Models, and Disease Classes. PMID:34026820
AnnotSV and knotAnnotSV: a web server for human structural variations annotations, ranking and analysis. PMID:34023905
COVID-19 biomarkers and their overlap with comorbidities in a disease biomarker data model. PMID:34015823
Inborn disorders of the malate aspartate shuttle. PMID:33990986
Craniofacial features of 3q29 deletion syndrome: Application of next-generation phenotyping technology. PMID:33938623
How to design a registry for undiagnosed patients in the framework of rare disease diagnosis: suggestions on software, data set and coding system. PMID:33933089
FMRP attenuates activity dependent modifications in the mitochondrial proteome. PMID:33931071
The Increasing Impact of Translational Research in the Molecular Diagnostics of Neuromuscular Diseases. PMID:33924139
The VRNetzer platform enables interactive network analysis in Virtual Reality. PMID:33893283
An EPIC predictor of gestational age and its application to newborns conceived by assisted reproductive technologies. PMID:33875015
GPCards: An integrated database of genotype-phenotype correlations in human genetic diseases. PMID:33868597
Towards enhanced understanding of idiopathic ketotic hypoglycemia: a literature review and introduction of the patient organization, Ketotic Hypoglycemia International. PMID:33849624
Improved characterisation of clinical text through ontology-based vocabulary expansion. PMID:33845909
MendelVar: gene prioritization at GWAS loci using phenotypic enrichment of Mendelian disease genes. PMID:33836063
Gene Set Knowledge Discovery with Enrichr. PMID:33780170
Novel bi-allelic variants expand the SPTBN4-related genetic and phenotypic spectrum. PMID:33772159
Modeling multifunctionality of genes with secondary gene co-expression networks in human brain provides novel disease insights. PMID:33734320
Towards realizing the vision of precision medicine: AI based prediction of clinical drug response. PMID:33734308
Computational analysis of 10,860 phenotypic annotations in individuals with SCN2A-related disorders. PMID:33731876
Underrepresentation of Phenotypic Variability of 16p13.11 Microduplication Syndrome Assessed With an Online Self-Phenotyping Tool (Phenotypr): Cohort Study. PMID:33724192
DeepViral: prediction of novel virus-host interactions from protein sequences and infectious disease phenotypes. PMID:33682875
Improving gene function predictions using independent transcriptional components. PMID:33674610
Novel variants in TUBA1A cause congenital fibrosis of the extraocular muscles with or without malformations of cortical brain development. PMID:33649541
Genetic spectrum and clinical early natural history of glucose-6-phosphate dehydrogenase deficiency in Mexican children detected through newborn screening. PMID:33637102
ClinSV: clinical grade structural and copy number variant detection from whole genome sequencing data. PMID:33632298
Genetic testing for unexplained perinatal disorders. PMID:33605625
Curation of over 10 000 transcriptomic studies to enable data reuse. PMID:33599246
Novel Variant Findings and Challenges Associated With the Clinical Integration of Genomic Testing: An Interim Report of the Genomic Medicine for Ill Neonates and Infants (GEMINI) Study. PMID:33587123
Commonalities across computational workflows for uncovering explanatory variants in undiagnosed cases. PMID:33580225
Compound Heterozygosity for a Novel Frameshift Variant Causing Fatal Infantile Liver Failure and Genotype-Phenotype Correlation of POLG c.3286C>T Variant. PMID:33562887
Mutation-specific pathophysiological mechanisms define different neurodevelopmental disorders associated with SATB1 dysfunction. PMID:33513338
The landscape of nutri-informatics: a review of current resources and challenges for integrative nutrition research. PMID:33494105
Detection of aberrant gene expression events in RNA sequencing data. PMID:33462443
Donor genetic variants as risk factors for thrombosis after liver transplantation: A genome-wide association study. PMID:33445220
Multiplex gene and phenotype network to characterize shared genetic pathways of epilepsy and autism. PMID:33441621
Systematic detection of brain protein-coding genes under positive selection during primate evolution and their roles in cognition. PMID:33441416
The variant call format provides efficient and robust storage of GWAS summary statistics. PMID:33441155
Artificial Intelligence in Drug Discovery: A Comprehensive Review of Data-driven and Machine Learning Approaches. PMID:33437151
Transcriptome profiling of insulin sensitive tissues from GH deficient mice following GH treatment. PMID:33433889
The case for open science: rare diseases. PMID:33426479
MicroPhenoDB Associates Metagenomic Data with Pathogenic Microbes, Microbial Core Genes, and Human Disease Phenotypes. PMID:33418085
Spatiotemporal analysis of human intestinal development at single-cell resolution. PMID:33406409
Actionable and incidental neuroradiological findings in twins with neurodevelopmental disorders. PMID:33376247
Multi-resolution visualization and analysis of biomolecular networks through hierarchical community detection and web-based graphical tools. PMID:33351828
A review on viral data sources and search systems for perspective mitigation of COVID-19. PMID:33348368
Coupling of autism genes to tissue-wide expression and dysfunction of synapse, calcium signalling and transcriptional regulation. PMID:33338084
Phenotypic and Genotypic Features of Thai Patients With Nonsyndromic Tooth Agenesis and WNT10A Variants. PMID:33329022
Outlier concepts auditing methodology for a large family of biomedical ontologies. PMID:33319713
DUOX2 variants are a frequent cause of congenital primary hypothyroidism in Thai patients. PMID:33310921
A flexible computational pipeline for research analyses of unsolved clinical exome cases. PMID:33303739
CovMulNet19, Integrating Proteins, Diseases, Drugs, and Symptoms: A Network Medicine Approach to COVID-19. PMID:33274348
The Human Phenotype Ontology in 2021. PMID:33264411
HERB: a high-throughput experiment- and reference-guided database of traditional Chinese medicine. PMID:33264402
Investigation of COVID-19 comorbidities reveals genes and pathways coincident with the SARS-CoV-2 viral disease. PMID:33257774
'There and Back Again'-Forward Genetics and Reverse Phenotyping in Pulmonary Arterial Hypertension. PMID:33256119
Gene-specific facial dysmorphism in Axenfeld-Rieger syndrome caused by FOXC1 and PITX2 variants. PMID:33231930
DeepPheno: Predicting single gene loss-of-function phenotypes using an ontology-aware hierarchical classifier. PMID:33206638
Natural language processing algorithms for mapping clinical text fragments onto ontology concepts: a systematic review and recommendations for future studies. PMID:33198814
A Collection of Benchmark Data Sets for Knowledge Graph-based Similarity in the Biomedical Domain. PMID:33181823
PK-DB: pharmacokinetics database for individualized and stratified computational modeling. PMID:33151297
The role of genomics and genetics in pulmonary arterial hypertension. PMID:33150157
Developmental Neurotoxicity of the Harmful Algal Bloom Toxin Domoic Acid: Cellular and Molecular Mechanisms Underlying Altered Behavior in the Zebrafish Model. PMID:33147070
Feature selection algorithm based on dual correlation filters for cancer-associated somatic variants. PMID:33121438
Prenatal diagnosis of Norrie disease after whole exome sequencing of an affected proband during an ongoing pregnancy: a case report. PMID:33092543
Predicting candidate genes from phenotypes, functions and anatomical site of expression. PMID:33051643
Semantic similarity and machine learning with ontologies. PMID:33049044
Practical guide to genetic screening for inherited eye diseases. PMID:33015543
Artificial intelligence and the hunt for immunological disorders. PMID:33002894
Phenotype-genotype comorbidity analysis of patients with rare disorders provides insight into their pathological and molecular bases. PMID:33001999
Investigation of COVID-19 comorbidities reveals genes and pathways coincident with the SARS-CoV-2 viral disease. PMID:32995795
Genome Sequencing as a Diagnostic Test in Children With Unexplained Medical Complexity. PMID:32960281
PAWER: protein array web exploreR. PMID:32942983
IDDB: a comprehensive resource featuring genes, variants and characteristics associated with infertility. PMID:32941628
Understanding microcephaly through the study of centrosome regulation in Drosophila neural stem cells. PMID:32897294
Ontological approach to the knowledge systematization of a toxic process and toxic course representation framework for early drug risk management. PMID:32883995
Computational Methods and Software Tools for Functional Analysis of miRNA Data. PMID:32872205
Systems Biology Approaches Reveal Potential Phenotype-Modifier Genes in Neurofibromatosis Type 1. PMID:32858845
Study on Intervention Mechanism of Yiqi Huayu Jiedu Decoction on ARDS Based on Network Pharmacology. PMID:32849901
Consequences of 22q11.2 Microdeletion on the Genome, Individual and Population Levels. PMID:32842603
Ontologies, Knowledge Representation, and Machine Learning for Translational Research: Recent Contributions. PMID:32823310
Expanding the phenotype of CRYAA nucleotide variants to a complex presentation of anterior segment dysgenesis. PMID:32791987
Interpretable Clinical Genomics with a Likelihood Ratio Paradigm. PMID:32755546
Phexpo: a package for bidirectional enrichment analysis of phenotypes and chemicals. PMID:32734156
CAMT-MPL: congenital amegakaryocytic thrombocytopenia caused by MPL mutations - heterogeneity of a monogenic disorder - a comprehensive analysis of 56 patients. PMID:32703794
Choosing preferable labels for the Japanese translation of the Human Phenotype Ontology. PMID:32634877
Improving accessibility and distinction between negative results in biomedical relation extraction. PMID:32634874
A proof-of-concept study of extracting patient histories for rare/intractable diseases from social media. PMID:32634871
Drosophila models of pathogenic copy-number variant genes show global and non-neuronal defects during development. PMID:32579612
Disrupted minor intron splicing is prevalent in Mendelian disorders. PMID:32573973
Transcriptome-Wide Regulation of Key Developmental Pathways in the Mouse Neural Tube by Prenatal Alcohol Exposure. PMID:32557641
A novel mosaic variant on SMC1A reported in buccal mucosa cells, albeit not in blood, of a patient with Cornelia de Lange-like presentation. PMID:32532882
Phen2Gene: rapid phenotype-driven gene prioritization for rare diseases. PMID:32500119
Revealing the Common Mechanisms of Scutellarin in Angina Pectoris and Ischemic Stroke Treatment via a Network Pharmacology Approach. PMID:32447519
Clinical Bioinformatics in Precise Diagnosis of Mitochondrial Disease. PMID:32439066
Applications of molecular networks in biomedicine. PMID:32395629
Applying knowledge-driven mechanistic inference to toxicogenomics. PMID:32387679
An Improved Phenotype-Driven Tool for Rare Mendelian Variant Prioritization: Benchmarking Exomiser on Real Patient Whole-Exome Data. PMID:32340307
RA-map: building a state-of-the-art interactive knowledge base for rheumatoid arthritis. PMID:32311035
genoDraw: A Web Tool for Developing Pedigree Diagrams Using the Standardized Human Pedigree Nomenclature Integrated with Biomedical Vocabularies. PMID:32308839
Prot2HG: a database of protein domains mapped to the human genome. PMID:32293014
Structured reviews for data and knowledge-driven research. PMID:32283553
Evaluation of the quality of clinical data collection for a pan-Canadian cohort of children affected by inherited metabolic diseases: lessons learned from the Canadian Inherited Metabolic Diseases Research Network. PMID:32276663
Genetic landscape of autism spectrum disorder in Vietnamese children. PMID:32193494
Limitations of exome sequencing in detecting rare and undiagnosed diseases. PMID:32190976
Genomic Landscape and Mutational Spectrum of ADAMTS Family Genes in Mendelian Disorders Based on Gene Evidence Review for Variant Interpretation. PMID:32183147
Expanding Clinical Presentations Due to Variations in THOC2 mRNA Nuclear Export Factor. PMID:32116545
Genetic Modifiers and Rare Mendelian Disease. PMID:32106447
Evaluating Face2Gene as a Tool to Identify Cornelia de Lange Syndrome by Facial Phenotypes. PMID:32033219
Significantly different clinical phenotypes associated with mutations in synthesis and transamidase+remodeling glycosylphosphatidylinositol (GPI)-anchor biosynthesis genes. PMID:32019583
Human and mouse essentiality screens as a resource for disease gene discovery. PMID:32005800
Incremental data integration for tracking genotype-disease associations. PMID:31986132
Monogenic causes of non-obstructive azoospermia: challenges, established knowledge, limitations and perspectives. PMID:31955275
Large-Scale Whole-Genome Sequencing Reveals the Genetic Architecture of Primary Membranoproliferative GN and C3 Glomerulopathy. PMID:31919107
Mechanistic insights into transcription factor cooperativity and its impact on protein-phenotype interactions. PMID:31913281
Genome analysis and knowledge-driven variant interpretation with TGex. PMID:31888639
Diagnostic yield of panel-based genetic testing in syndromic inherited retinal disease. PMID:31836858
Prioritization of genes driving congenital phenotypes of patients with de novo genomic structural variants. PMID:31801603
The Hearing Impairment Ontology: A Tool for Unifying Hearing Impairment Knowledge to Enhance Collaborative Research. PMID:31766582
Semantic computational analysis of anticoagulation use in atrial fibrillation from real world data. PMID:31765395
Artificial intelligence in clinical and genomic diagnostics. PMID:31744524
Representing glycophenotypes: semantic unification of glycobiology resources for disease discovery. PMID:31735951
Comorbidity of asthma and hypertension may be mediated by shared genetic dysregulation and drug side effects. PMID:31705029
The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species. PMID:31701156
Gene- and Disease-Based Expansion of the Knowledge on Inborn Errors of Immunity. PMID:31695696
From cytogenetics to cytogenomics: whole-genome sequencing as a first-line test comprehensively captures the diverse spectrum of disease-causing genetic variation underlying intellectual disability. PMID:31694722
A new mutation in the PAX2 gene in a Papillorenal Syndrome patient. PMID:31692565
The DisGeNET knowledge platform for disease genomics: 2019 update. PMID:31680165
A multi-omics digital research object for the genetics of sleep regulation. PMID:31672980
Ensembles of natural language processing systems for portable phenotyping solutions. PMID:31655273
Genes essential for embryonic stem cells are associated with neurodevelopmental disorders. PMID:31649057
Gene4Denovo: an integrated database and analytic platform for de novo mutations in humans. PMID:31642496
WormBase: a modern Model Organism Information Resource. PMID:31642470
PhenoModifier: a genetic modifier database for elucidating the genetic basis of human phenotypic variation. PMID:31642469
VarSight: prioritizing clinically reported variants with binary classification algorithms. PMID:31615419
GWAS Central: a comprehensive resource for the discovery and comparison of genotype and phenotype data from genome-wide association studies. PMID:31612961
Comparison of Causative Variant Prioritization Tools Using Next-generation Sequencing Data in Japanese Patients with Mendelian Disorders. PMID:31582890
Encoding Clinical Data with the Human Phenotype Ontology for Computational Differential Diagnostics. PMID:31479590
Phenome-wide Burden of Copy-Number Variation in the UK Biobank. PMID:31353025
GAA variants and phenotypes among 1,079 patients with Pompe disease: Data from the Pompe Registry. PMID:31342611
Re-curation and rational enrichment of knowledge graphs in Biological Expression Language. PMID:31225582
Using phenome-wide association studies to examine the effect of environmental exposures on human health. PMID:31200158
VCF/Plotein: visualization and prioritization of genomic variants from human exome sequencing projects. PMID:31161195
New models for human disease from the International Mouse Phenotyping Consortium. PMID:31127358
Semantic integration of clinical laboratory tests from electronic health records for deep phenotyping and biomarker discovery. PMID:31119199
RegulationSpotter: annotation and interpretation of extratranscriptic DNA variants. PMID:31106382
Doc2Hpo: a web application for efficient and accurate HPO concept curation. PMID:31106327
g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update). PMID:31066453
Specific phenotype semantics facilitate gene prioritization in clinical exome sequencing. PMID:31053788
Identifying Disease-Gene Associations With Graph-Regularized Manifold Learning. PMID:31001321
Uncovering Missing Heritability in Rare Diseases. PMID:30987386
Measuring the importance of vertices in the weighted human disease network. PMID:30901770
ClinTAD: a tool for copy number variant interpretation in the context of topologically associated domains. PMID:30765865
The human phenotype ontology PubMed citations: 123.

123 articles citing: The human phenotype ontology

Predicting genes from phenotypes using human phenotype ontology (HPO) terms. PMID:35357580
The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development. PMID:35317743
A multi-network integration approach for measuring disease similarity based on ncRNA regulation and heterogeneous information. PMID:35255810
An ontology network for Diabetes Mellitus in Mexico. PMID:34625104
Shifting Gears in Precision Oncology-Challenges and Opportunities of Integrative Data Analysis. PMID:34572523
RDmap: a map for exploring rare diseases. PMID:33632281
Establishment and application of information resource of mutant mice in RIKEN BioResource Research Center. PMID:33455583
Phenotypically Similar Rare Disease Identification from an Integrative Knowledge Graph for Data Harmonization: Preliminary Study. PMID:33006565
Modelling kidney disease using ontology: insights from the Kidney Precision Medicine Project. PMID:32939051
Systematic identification of genetic systems associated with phenotypes in patients with rare genomic copy number variations. PMID:32778951
Ontological Organization and Bioinformatic Analysis of Adverse Drug Reactions From Package Inserts: Development and Usability Study. PMID:32706718
TarGo: network based target gene selection system for human disease related mouse models. PMID:32257911
Study of the Gastrointestinal Heat Retention Syndrome in Children: From Diagnostic Model to Biological Basis. PMID:31929814
Computational Methods for Identifying Similar Diseases. PMID:31678735
Data-driven method to enhance craniofacial and oral phenotype vocabularies. PMID:31668172
Encoding Clinical Data with the Human Phenotype Ontology for Computational Differential Diagnostics. PMID:31479590
Closing the 'phenotype gap' in precision medicine: improving what we measure to understand complex disease mechanisms. PMID:31428846
From Big Data to Precision Medicine. PMID:30881956
Integrating ontologies of human diseases, phenotypes, and radiological diagnosis. PMID:30624645
From scientific discovery to treatments for rare diseases - the view from the National Center for Advancing Translational Sciences - Office of Rare Diseases Research. PMID:30400963
The value of genomic variant ClinVar submissions from clinical providers: Beyond the addition of novel variants. PMID:30311381
ClinGen's GenomeConnect registry enables patient-centered data sharing. PMID:30311371
Utilization of Electronic Medical Records and Biomedical Literature to Support the Diagnosis of Rare Diseases Using Data Fusion and Collaborative Filtering Approaches. PMID:30305261
Computational resources associating diseases with genotypes, phenotypes and exposures. PMID:30102366
Enumerating consistent sub-graphs of directed acyclic graphs: an insight into biomedical ontologies. PMID:29949985
Phenotype-loci associations in networks of patients with rare disorders: application to assist in the diagnosis of novel clinical cases. PMID:29946186
Efficient Non-viral Gene Delivery into Human Hematopoietic Stem Cells by Minicircle Sleeping Beauty Transposon Vectors. PMID:29503198
A phenotype centric benchmark of variant prioritisation tools. PMID:29423277
InfAcrOnt: calculating cross-ontology term similarities using information flow by a random walk. PMID:29363423
Computer face-matching technology using two-dimensional photographs accurately matches the facial gestalt of unrelated individuals with the same syndromic form of intellectual disability. PMID:29258477
Linked Registries: Connecting Rare Diseases Patient Registries through a Semantic Web Layer. PMID:29214177
A rare variant in the FHL1 gene associated with X-linked recessive hypoparathyroidism. PMID:28444561
The druggable genome and support for target identification and validation in drug development. PMID:28356508
Genomic variants reveal differential evolutionary constraints on human transglutaminases and point towards unrecognized significance of transglutaminase 2. PMID:28248968
Whole genome sequencing of one complex pedigree illustrates challenges with genomic medicine. PMID:28228131
OAHG: an integrated resource for annotating human genes with multi-level ontologies. PMID:27703231
An expanded evaluation of protein function prediction methods shows an improvement in accuracy. PMID:27604469
Design, construction, and technical implementation of a web-based interdisciplinary symptom evaluation (WISE) - a heuristic proposal for orofacial pain and temporomandibular disorders. PMID:27581159
Searching for rare diseases in PubMed: a blind comparison of Orphanet expert query and query based on terminological knowledge. PMID:27484923
Protein function in precision medicine: deep understanding with machine learning. PMID:27423136
Mutations specific to the Rac-GEF domain of TRIO cause intellectual disability and microcephaly. PMID:27418539
Leveraging Comparative Genomics to Identify and Functionally Characterize Genes Associated with Sperm Phenotypes in Python bivittatus (Burmese Python). PMID:27200191
Recommendations for the integration of genomics into clinical practice. PMID:27171546
Phenotype-driven gene target definition in clinical genome-wide sequencing data interpretation. PMID:27031083
Genomic insights into ayurvedic and western approaches to personalized medicine. PMID:27019453
LORD: a phenotype-genotype semantically integrated biomedical data tool to support rare disease diagnosis coding in health information systems. PMID:26958175
Semantic representation of reported measurements in radiology. PMID:26801764
EHR based Genetic Testing Knowledge Base (iGTKB) Development. PMID:26606281
Systematic analysis of copy number variants of a large cohort of orofacial cleft patients identifies candidate genes for orofacial clefts. PMID:26561393
Actionable clinical decisions based on comprehensive genomic evaluation in asymptomatic adults. PMID:26436109
Diagnostic interpretation of array data using public databases and internet sources. PMID:26285306
Facilitating collaboration in rare genetic disorders through effective matchmaking in DECIPHER. PMID:26220709
Exome sequencing analysis reveals variants in primary immunodeficiency genes in patients with very early onset inflammatory bowel disease. PMID:26193622
Phenolyzer: phenotype-based prioritization of candidate genes for human diseases. PMID:26192085
GenomeConnect: matchmaking between patients, clinical laboratories, and researchers to improve genomic knowledge. PMID:26178529
How to build personalized multi-omics comorbidity profiles. PMID:26157799
DNAseq Workflow in a Diagnostic Context and an Example of a User Friendly Implementation. PMID:26137478
A bioinformatics expert system linking functional data to anatomical outcomes in limb regeneration. PMID:25729585
Duplications in ADHD patients harbour neurobehavioural genes that are co-expressed with genes associated with hyperactivity in the mouse. PMID:25656289
Next-generation sequencing-based genome diagnostics across clinical genetics centers: implementation choices and their effects. PMID:25626705
Phenomics research on coronary heart disease based on human phenotype ontology. PMID:25610858
POEAS: Automated Plant Phenomic Analysis Using Plant Ontology. PMID:25574136
Finding our way through phenotypes. PMID:25562316
Genetic diagnosis of developmental disorders in the DDD study: a scalable analysis of genome-wide research data. PMID:25529582
Capturing the clinical utility of genomic testing: medical recommendations following pediatric microarray. PMID:25491637
PhenUMA: a tool for integrating the biomedical relationships among genes and diseases. PMID:25420641
The Human Variome Project: ensuring the quality of DNA variant databases in inherited renal disease. PMID:25384529
VariantDB: a flexible annotation and filtering portal for next generation sequencing data. PMID:25352915
Whole exome sequencing in family trios reveals de novo mutations in PURA as a cause of severe neurodevelopmental delay and learning disability. PMID:25342064
A test for ancient selective sweeps and an application to candidate sites in modern humans. PMID:25172957
EHR Big Data Deep Phenotyping. Contribution of the IMIA Genomic Medicine Working Group. PMID:25123744
GrabBlur--a framework to facilitate the secure exchange of whole-exome and -genome SNV data using VCF files. PMID:25055742
Clinical phenotype-based gene prioritization: an initial study using semantic similarity and the human phenotype ontology. PMID:25047600
A methodology for a minimum data set for rare diseases to support national centers of excellence for healthcare and research. PMID:25038198
Large scale analysis of phenotype-pathway relationships based on GWAS results. PMID:25007247
Network based integrated analysis of phenotype-genotype data for prioritization of candidate symptom genes. PMID:24991551
SemFunSim: a new method for measuring disease similarity by integrating semantic and gene functional association. PMID:24932637
Changing genetic paradigms: creating next-generation genetic databases as tools to understand the emerging complexities of genotype/phenotype relationships. PMID:24885908
Patterns of coding variation in the complete exomes of three Neandertals. PMID:24753607
Exome sequencing improves genetic diagnosis of structural fetal abnormalities revealed by ultrasound. PMID:24476948
NCBI disease corpus: a resource for disease name recognition and concept normalization. PMID:24393765
The NHGRI GWAS Catalog, a curated resource of SNP-trait associations. PMID:24316577
Inference of gene-phenotype associations via protein-protein interaction and orthology. PMID:24194887
Learning to recognize phenotype candidates in the auto-immune literature using SVM re-ranking. PMID:24155869
DECIPHER: database for the interpretation of phenotype-linked plausibly pathogenic sequence and copy-number variation. PMID:24150940
The Drosophila phenotype ontology. PMID:24138933
The ontology of craniofacial development and malformation for translational craniofacial research. PMID:24124010
Human disease locus discovery and mapping to molecular pathways through phylogenetic profiling. PMID:24084807
Manteia, a predictive data mining system for vertebrate genes and its applications to human genetic diseases. PMID:24038354
The mouse pathology ontology, MPATH; structure and applications. PMID:24033988
A candidate gene approach for virally induced cancer with application to HIV-related Kaposi's sarcoma. PMID:23818101
A knowledge based approach to matching human neurodegenerative disease and animal models. PMID:23717278
A two-level model for the analysis of syndrome of acute ischemic stroke: from diagnostic model to molecular mechanism. PMID:23662126
Neurocarta: aggregating and sharing disease-gene relations for the neurosciences. PMID:23442263
Global analysis of the human pathophenotypic similarity gene network merges disease module components. PMID:23437198
Towards a bioinformatics of patterning: a computational approach to understanding regulative morphogenesis. PMID:23429669
STOP using just GO: a multi-ontology hypothesis generation tool for high throughput experimentation. PMID:23409969
Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers. PMID:23340843
Semantically enabling a genome-wide association study database. PMID:23244533
DbVar and DGVa: public archives for genomic structural variation. PMID:23193291
Phenotypic overlap in the contribution of individual genes to CNV pathogenicity revealed by cross-species computational analysis of single-gene mutations in humans, mice and zebrafish. PMID:23104991
VarioML framework for comprehensive variation data representation and exchange. PMID:23031277
Sequence thyself: personalized medicine and therapies for the future: 2012 Yale Healthcare Conference. PMID:23012590
DECIPHER: web-based, community resource for clinical interpretation of rare variants in developmental disorders. PMID:22962312
Process attributes in bio-ontologies. PMID:22928880
Querying phenotype-genotype relationships on patient datasets using semantic web technology: the example of Cerebrotendinous xanthomatosis. PMID:22849591
Co-clustering phenome-genome for phenotype classification and disease gene discovery. PMID:22735708
Three ontologies to define phenotype measurement data. PMID:22654893
The laboratory-clinician team: a professional call to action to improve communication and collaboration for optimal patient care in chromosomal microarray testing. PMID:22610653
MSV3d: database of human MisSense Variants mapped to 3D protein structure. PMID:22491796
Phenotypic information in genomic variant databases enhances clinical care and research: the International Standards for Cytogenomic Arrays Consortium experience. PMID:22331816
Disease Ontology: a backbone for disease semantic integration. PMID:22080554
Improving ontologies by automatic reasoning and evaluation of logical definitions. PMID:22032770
Clarity and claims in variation/mutation databasing. PMID:21904316
The RICORDO approach to semantic interoperability for biomedical data and models: strategy, standards and solutions. PMID:21878109
PREDICT: a method for inferring novel drug indications with application to personalized medicine. PMID:21654673
g:Profiler--a web server for functional interpretation of gene lists (2011 update). PMID:21646343
The FaceBase Consortium: a comprehensive program to facilitate craniofacial research. PMID:21458441
Transactional database transformation and its application in prioritizing human disease genes. PMID:21422495
CSI-OMIM--Clinical Synopsis Search in OMIM. PMID:21362185
The RIKEN integrated database of mammals. PMID:21076152
An introduction to standardized clinical nomenclature for dysmorphic features: the Elements of Morphology project. PMID:20920337
A standard variation file format for human genome sequences. PMID:20796305

http://human-phenotype-ontology.github.io/license.html

http://dx.doi.org/10.1093/nar/gkaa1043

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disease
metasource: Fairsharing.org
version: FAIRsharing.org: HP; Human Phenotype Ontology; DOI: https://doi.org/10.25504/FAIRsharing.kbtt7f; Last edited: July 9, 2019, 10:37 a.m.; Last accessed: Jan 03 2022 7:12 p.m.

phenotype
metasource: Fairsharing.org
version: FAIRsharing.org: HP; Human Phenotype Ontology; DOI: https://doi.org/10.25504/FAIRsharing.kbtt7f; Last edited: July 9, 2019, 10:37 a.m.; Last accessed: Jan 03 2022 7:12 p.m.

genomics databases (non-vertebrate)
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

genome annotation terms, ontologies and nomenclature
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

genotype and phenotype
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:43.873620

ontology and terminology
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:43.873620

human biology
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:43.873620

literature and language
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:43.873620

rare diseases
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:43.873620

disease phenotype genomics genome annotation terms, ontologies and nomenclature genotype and phenotype ontology and terminology human literature and language rare diseases

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Online Mendelian Inheritance in Man Ontology

HPO - ORDO Ontological Module

Online Mendelian Inheritance in Man

Cerebrotendinous Xanthomatosis Ontology

Disease Ontology

PhenoDis

Dictyostelium Phenotype Ontology

Cell Phenotype Ontology

Orphanet Rare Diseases Ontology

Ascomycete Phenotype Ontology

Online Mendelian Inheritance in Animals

Reproductive trait and phenotype ontology

Zebrafish Phenotype Ontology

Placental Maternal Health Conditions

Ontology of Microbial Phenotypes

Planarian Phenotype Ontology

Flora Phenotype Ontology

Resource of Asian Primary Immunodeficiency Diseases Phenotype Ontology

SAMS

Combined Phenotype Ontology