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Human genotype–phenotype databases: aims, challenges and opportunities
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Outgoing claims: the papers this work cites, builds on, or argues with.
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UMD (Universal Mutation Database): A generic software to build and analyze locus-specific databases
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A suggested nomenclature for designating mutations
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Immunodeficiency mutation databases (IDbases)
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Improving sequence variant descriptions in mutation databases and literature using the Mutalyzer sequence variation nomenclature checker
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Sequence variant classification and reporting: recommendations for improving the interpretation of cancer susceptibility genetic test results
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Describing structural changes by extending HGVS sequence variation nomenclature
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LOVD v.2.0: the next generation in gene variant databases
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A new face and new challenges for Online Mendelian Inheritance in Man (OMIM®)
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Mandatory variant submission-Our experiences
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Phenotypic information in genomic variant databases enhances clinical care and research: The international standards for cytogenomic arrays consortium experience
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Standard terminology for phenotypic variations: The Elements of Morphology project, its current progress, and future directions
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Observ-OM and Observ-TAB: Universal syntax solutions for the integration, search, and exchange of phenotype and genotype information
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Representation of rare diseases in health information systems: The orphanet approach to serve a wide range of end users
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Human variome project country nodes: Documenting genetic information within a country
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ALSoD: A user-friendly online bioinformatics tool for amyotrophic lateral sclerosis genetics
inferredcites →https://doi.org/10.1002/humu.22283openalex-snapshot
P heno DB : A New Web‐Based Tool for the Collection, Storage, and Analysis of Phenotypic Features
inferredcites →https://doi.org/10.1002/humu.22305openalex-snapshot
GEnomes Management Application (GEM.app): A New Software Tool for Large-Scale Collaborative Genome Analysis
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The Finnish Disease Heritage Database (FinDis) Update-A Database for the Genes Mutated in the Finnish Disease Heritage Brought to the Next-Generation Sequencing Era
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GeneYenta: A PhenotypeBased Rare Disease Case Matching Tool Based on Online Dating Algorithms for the Acceleration of Exome Interpretation
inferredcites →https://doi.org/10.1002/humu.22838openalex-snapshot
GenomeConnect: Matchmaking Between Patients, Clinical Laboratories, and Researchers to Improve Genomic Knowledge
inferredcites →https://doi.org/10.1002/humu.22841openalex-snapshot
Cafe Variome: General-Purpose Software for Making Genotype-Phenotype Data Discoverable in Restricted or Open Access Contexts
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GeneMatcher: A Matching Tool for Connecting Investigators with an Interest in the Same Gene
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PhenomeCentral: A Portal for Phenotypic and Genotypic Matchmaking of Patients with Rare Genetic Diseases
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Use of Model Organism and Disease Databases to Support Matchmaking for Human Disease Gene Discovery
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The Matchmaker Exchange: A Platform for Rare Disease Gene Discovery
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Nomenclature for the description of human sequence variations
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RD-Connect: An Integrated Platform Connecting Databases, Registries, Biobanks and Clinical Bioinformatics for Rare Disease Research
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DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources
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Actionable, Pathogenic Incidental Findings in 1,000 Participants’ Exomes
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Phevor Combines Multiple Biomedical Ontologies for Accurate Identification of Disease-Causing Alleles in Single Individuals and Small Nuclear Families
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FORGE Canada Consortium: Outcomes of a 2-Year National Rare-Disease Gene-Discovery Project
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The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease
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Patient empowerment—who empowers whom?
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Genetic diagnosis of developmental disorders in the DDD study: a scalable analysis of genome-wide research data
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Geneticists push for global data-sharing
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Pharmacogenomics Knowledge for Personalized Medicine
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GWAS Central: a comprehensive resource for the comparison and interrogation of genome-wide association studies
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International Charter of principles for sharing bio-specimens and data
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Genome-wide association database developed in the Japanese Integrated Database Project
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International network of cancer genome projects
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A map of human genome variation from population-scale sequencing
inferredcites →https://doi.org/10.1038/nbt.2749openalex-snapshot
Systematic comparison of phenome-wide association study of electronic medical record data and genome-wide association study data
inferredcites →https://doi.org/10.1038/ng.2745openalex-snapshot
Defining the disease liability of variants in the cystic fibrosis transmembrane conductance regulator gene
inferredcites →https://doi.org/10.1038/ng.2764openalex-snapshot
The Cancer Genome Atlas Pan-Cancer analysis project
inferredcites →https://doi.org/10.1038/ng.3312openalex-snapshot
The European Genome-phenome Archive of human data consented for biomedical research
inferredcites →https://doi.org/10.1038/ng0407-425openalex-snapshot
A database of locus-specific databases
inferredcites →https://doi.org/10.1038/ng0407-427openalex-snapshot
Analysis of published PKD1 gene sequence variants
inferredcites →https://doi.org/10.1038/nmeth.2656openalex-snapshot
eXtasy: variant prioritization by genomic data fusion
inferredcites →https://doi.org/10.1038/nmeth.3046openalex-snapshot
Phen-Gen: combining phenotype and genotype to analyze rare disorders
inferredcites →https://doi.org/10.1038/nrg2999openalex-snapshot
Using electronic health records to drive discovery in disease genomics
inferredcites →https://doi.org/10.1038/nrg3046openalex-snapshot
Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data
inferredcites →https://doi.org/10.1038/nrg3463openalex-snapshot
Disease-targeted sequencing: a cornerstone in the clinic
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Cooperative control of striated muscle mass and metabolism by MuRF1 and MuRF2
inferredcites →https://doi.org/10.1056/nejmoa1306555openalex-snapshot
Clinical Whole-Exome Sequencing for the Diagnosis of Mendelian Disorders
inferredcites →https://doi.org/10.1056/nejmsr1406261openalex-snapshot
ClinGen — The Clinical Genome Resource
inferredcites →https://doi.org/10.1073/pnas.1201904109openalex-snapshot
A public resource facilitating clinical use of genomes
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/btr330openalex-snapshot
The variant call format and VCFtools
inferredcites →https://doi.org/10.1093/bioinformatics/btr540openalex-snapshot
Kaviar: an accessible system for testing SNV novelty
inferredcites →https://doi.org/10.1093/bioinformatics/btu630openalex-snapshot
A Python package for parsing, validating, mapping and formatting sequence variants using HGVS nomenclature
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International Cancer Genome Consortium Data Portal--a one-stop shop for cancer genomics data
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MalaCards: an integrated compendium for diseases and their annotation
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The Cancer Genomics Hub (CGHub): overcoming cancer through the power of torrential data
inferredcites →https://doi.org/10.1093/hmg/ddt384openalex-snapshot
Databases of genomic variation and phenotypes: existing resources and future needs
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DataSHIELD: taking the analysis to the data, not the data to the analysis
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The human type I collagen mutation database
inferredcites →https://doi.org/10.1093/nar/gkl927openalex-snapshot
An enhanced MITOMAP with a global mtDNA mutational phylogeny
inferredcites →https://doi.org/10.1093/nar/gkp1137openalex-snapshot
The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants
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COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer
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GWASdb: a database for human genetic variants identified by genome-wide association studies
inferredcites →https://doi.org/10.1093/nar/gkr798openalex-snapshot
SNPedia: a wiki supporting personal genome annotation, interpretation and analysis
inferredcites →https://doi.org/10.1093/nar/gkt1025openalex-snapshot
DriverDB: an exome sequencing database for cancer driver gene identification
inferredcites →https://doi.org/10.1093/nar/gkt1026openalex-snapshot
The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data
inferredcites →https://doi.org/10.1093/nar/gkt1113openalex-snapshot
ClinVar: public archive of relationships among sequence variation and human phenotype
inferredcites →https://doi.org/10.1093/nar/gkt1125openalex-snapshot
Developments in FINDbase worldwide database for clinically relevant genomic variation allele frequencies
inferredcites →https://doi.org/10.1093/nar/gkt1198openalex-snapshot
Locus Reference Genomic: reference sequences for the reporting of clinically relevant sequence variants
inferredcites →https://doi.org/10.1093/nar/gkt1211openalex-snapshot
NCBI’s Database of Genotypes and Phenotypes: dbGaP
inferredcites →https://doi.org/10.1093/nar/gkt1229openalex-snapshot
The NHGRI GWAS Catalog, a curated resource of SNP-trait associations
inferredcites →https://doi.org/10.1093/nar/gkt937openalex-snapshot
DECIPHER: database for the interpretation of phenotype-linked plausibly pathogenic sequence and copy-number variation
inferredcites →https://doi.org/10.1093/nar/gku1011openalex-snapshot
Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data
inferredcites →https://doi.org/10.1101/gr.157495.113openalex-snapshot
Variation Ontology for annotation of variation effects and mechanisms
inferredcites →https://doi.org/10.1101/gr.160325.113openalex-snapshot
Improved exome prioritization of disease genes through cross-species phenotype comparison
inferredcites →https://doi.org/10.1111/cge.12464openalex-snapshot
Whole‐exome sequencing broadens the phenotypic spectrum of rare pediatric epilepsy: a retrospective study
inferredcites →https://doi.org/10.1111/cge.12520openalex-snapshot
Patient reported outcomes and patient empowerment in clinical genetics services
inferredcites →https://doi.org/10.1126/science.1215040openalex-snapshot
A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes
inferredcites →https://doi.org/10.1126/science.1219240openalex-snapshot
Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes
inferredcites →https://doi.org/10.1126/scitranslmed.3001756openalex-snapshot
Carrier Testing for Severe Childhood Recessive Diseases by Next-Generation Sequencing
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Rapid Whole-Genome Sequencing for Genetic Disease Diagnosis in Neonatal Intensive Care Units
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Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome
inferredcites →https://doi.org/10.1126/scitranslmed.3010272openalex-snapshot
Phenomics and the Interpretation of Personal Genomes
inferredcites →https://doi.org/10.1126/scitranslmed.aab0194openalex-snapshot
Global implementation of genomic medicine: We are not alone
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Serving the enterprise and beyond with informatics for integrating biology and the bedside (i2b2)
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Human Gene Mutation Database: towards a comprehensive central mutation database
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Molecular Mechanisms of Stress-Responsive Changes in Collagen and Elastin Networks in Skin
inferredcites →https://doi.org/10.1161/01.cir.0000135582.53444.87openalex-snapshot
Prothrombin 20210 Mutation (Factor II Mutation)
inferredcites →https://doi.org/10.1161/circresaha.112.270207openalex-snapshot
Human Molecular Genetic and Functional Studies Identify TRIM63 , Encoding Muscle RING Finger Protein 1, as a Novel Gene for Human Hypertrophic Cardiomyopathy
inferredcites →https://doi.org/10.1161/circresaha.114.302662openalex-snapshot
Does p.Q247X in TRIM63 Cause Human Hypertrophic Cardiomyopathy?
inferredcites →https://doi.org/10.1182/blood-2012-12-474585openalex-snapshot
Massively parallel sequencing, aCGH, and RNA-Seq technologies provide a comprehensive molecular diagnosis of Fanconi anemia
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A formalized description of the standard human variant nomenclature in Extended Backus-Naur Form
inferredcites →https://doi.org/10.1186/1471-2105-13-254openalex-snapshot
VarioML framework for comprehensive variation data representation and exchange
inferredcites →https://doi.org/10.1186/gm145openalex-snapshot
Locus Reference Genomic sequences: an improved basis for describing human DNA variants
inferredcites →https://doi.org/10.1186/s11568-014-0003-1openalex-snapshot
Framework for responsible sharing of genomic and health-related data
inferredcites →https://doi.org/10.1186/s13073-015-0151-5openalex-snapshot
Human phenotype ontology annotation and cluster analysis to unravel genetic defects in 707 cases with unexplained bleeding and platelet disorders
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Secure, Privacy-Preserving Analysis of Distributed Databases
inferredcites →https://doi.org/10.1371/journal.pgen.1001111openalex-snapshot
The Characterization of Twenty Sequenced Human Genomes
inferredcites →https://doi.org/10.1371/journal.pgen.1003143openalex-snapshot
Predicting Mendelian Disease-Causing Non-Synonymous Single Nucleotide Variants in Exome Sequencing Studies
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Characterizing Race/Ethnicity and Genetic Ancestry for 100,000 Subjects in the Genetic Epidemiology Research on Adult Health and Aging (GERA) Cohort
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Sharing Health Data for Better Outcomes on PatientsLikeMe
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C-A3-04: The Kaiser Permanente Research Program on Genes, Environment and Health: A Resource for Genetic Epidemiology in Adult Health and Aging
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Disease advocacy organizations catalyze translational research
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Enhancing Discoverability of Public Health and Epidemiology Research Data
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Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Cross-Validation of Conserved Osteoblast-Specific Enhancers Illuminates Bone Diseases and Early Skeletal Evolution
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Variation Interpretation Predictors: Principles, Types, Performance, and Choice
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Chinese Medicine Phenomics (Chinmedphenomics): Personalized, Precise and Promising
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International Cooperation to Enable the Diagnosis of All Rare Genetic Diseases
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Doc2Hpo: a web application for efficient and accurate HPO concept curation
inferred← citeshttps://doi.org/10.1093/scipol/scaa011openalex-snapshot
Prospect patents, data markets, and the commons in data-driven medicine: Openness and the political economy of intellectual property rights
inferred← citeshttps://doi.org/10.1093/scipol/scaf039openalex-snapshot
The need for robust, FAIR phenomic databases supporting agricultural efficiency and resiliency
inferred← citeshttps://doi.org/10.1097/wno.0000000000001352openalex-snapshot
Dominant Optic Atrophy: How to Determine the Pathogenicity of Novel Variants?
inferred← citeshttps://doi.org/10.1101/2020.07.01.181677openalex-snapshot
Trantrace: a reliable, traceable, and collaborative solution to streamline the translation of emerging biomedical resources
inferred← citeshttps://doi.org/10.1101/2023.01.11.22283790openalex-snapshot
SwissGenVar : A platform for clinical grade interpretation of genetic variants to foster personalized health care in Switzerland
inferred← citeshttps://doi.org/10.1101/2023.08.30.555543openalex-snapshot
Architecture and evolutionary conservation of Xenopus tropicalis osteoblast-specific regulatory regions shed light on bone diseases and early skeletal evolution
inferred← citeshttps://doi.org/10.1109/iccoins.2016.7783250openalex-snapshot
Semantic ontology for annotated images
inferred← citeshttps://doi.org/10.1109/jbhi.2022.3177421openalex-snapshot
PIAT: An Evolutionarily Intelligent System for Deep Phenotyping of Chinese Electronic Health Records
inferred← citeshttps://doi.org/10.1109/jbhi.2025.3529598openalex-snapshot
PhenoAlign: A Hybrid Data-Knowledge-Driven Approach for Precisely Aligning Phenotype Information in Medical Texts
inferred← citeshttps://doi.org/10.1111/1471-0528.17561openalex-snapshot
Copy number variants and fetal structural abnormalities in stillborn fetuses: A secondary analysis of the Stillbirth Collaborative Research Network study
inferred← citeshttps://doi.org/10.1111/obr.12770openalex-snapshot
Established and emerging strategies to crack the genetic code of obesity
inferred← citeshttps://doi.org/10.1128/aac.00948-23openalex-snapshot
Therapeutic effect of iturin A on Candida albicans oral infection and its pathogenic factors
inferred← citeshttps://doi.org/10.1134/s1022795418010076openalex-snapshot
Use of Genotypes of Common Variants for Genome-Wide Regional Association Analysis
inferred← citeshttps://doi.org/10.1146/annurev-animal-020518-114913openalex-snapshot
Functional Annotation of Animal Genomes (FAANG): Current Achievements and Roadmap
inferred← citeshttps://doi.org/10.1161/circresaha.116.308996openalex-snapshot
Heart Failure in Pediatric Patients With Congenital Heart Disease
inferred← citeshttps://doi.org/10.1186/s12859-019-2801-xopenalex-snapshot
Automated assessment of biological database assertions using the scientific literature
inferred← citeshttps://doi.org/10.1186/s12864-016-2726-yopenalex-snapshot
Large scale analysis of protein stability in OMIM disease related human protein variants
inferred← citeshttps://doi.org/10.1186/s12931-017-0631-9openalex-snapshot
Using omics approaches to understand pulmonary diseases
inferred← citeshttps://doi.org/10.1186/s13023-019-1187-1openalex-snapshot
OPA1: 516 unique variants and 831 patients registered in an updated centralized Variome database
inferred← citeshttps://doi.org/10.1186/s13059-016-1102-1openalex-snapshot
Revisiting the morbid genome of Mendelian disorders
inferred← citeshttps://doi.org/10.1186/s13059-021-02442-8openalex-snapshot
VariantStore: an index for large-scale genomic variant search
inferred← citeshttps://doi.org/10.12681/plogos.27909openalex-snapshot
Ο Ρόλος των Βιολογικών και Γενετικών Παραγόντων στο Επίπεδο της Ευφυΐας
inferred← citeshttps://doi.org/10.12688/f1000research.10788.1openalex-snapshot
Recent advances in predicting gene–disease associations
inferred← citeshttps://doi.org/10.12688/f1000research.12344.1openalex-snapshot
Best practice data life cycle approaches for the life sciences
inferred← citeshttps://doi.org/10.1360/ssv-2023-0038openalex-snapshot
Development and application of rare diseases biobank
inferred← citeshttps://doi.org/10.1371/journal.pone.0162801openalex-snapshot
ePGA: A Web-Based Information System for Translational Pharmacogenomics
inferred← citeshttps://doi.org/10.1371/journal.pone.0164569openalex-snapshot
ODMSummary: A Tool for Automatic Structured Comparison of Multiple Medical Forms Based on Semantic Annotation with the Unified Medical Language System
inferred← citeshttps://doi.org/10.1513/annalsats.201810-716wsopenalex-snapshot
High-Throughput Sequencing in Respiratory, Critical Care, and Sleep Medicine Research. An Official American Thoracic Society Workshop Report
inferred← citeshttps://doi.org/10.20944/preprints202302.0452.v1openalex-snapshot
Inferring Neurocognition and Intelligence using Brain MRI
inferred← citeshttps://doi.org/10.20944/preprints202302.0452.v2openalex-snapshot
Inferring Neurocognition and Intelligence using Brain MRI
inferred← citeshttps://doi.org/10.2196/26892openalex-snapshot
Constructing High-Fidelity Phenotype Knowledge Graphs for Infectious Diseases With a Fine-Grained Semantic Information Model: Development and Usability Study
inferred← citeshttps://doi.org/10.25781/kaust-y5g20openalex-snapshot
Semantic Prioritization of Novel Causative Genomic Variants in Mendelian and Oligogenic Diseases
inferred← citeshttps://doi.org/10.26508/lsa.202403028openalex-snapshot
Human genetic variants in SLC39A8 impact uptake and steady-state metal levels within the cell
inferred← citeshttps://doi.org/10.3389/fcvm.2016.00022openalex-snapshot
The Current Landscape of Genetic Testing in Cardiovascular Malformations: Opportunities and Challenges
inferred← citeshttps://doi.org/10.3389/fgene.2018.00238openalex-snapshot
Application of Causal Inference to Genomic Analysis: Advances in Methodology
inferred← citeshttps://doi.org/10.3389/fgene.2022.981005openalex-snapshot
Computational approaches for predicting variant impact: An overview from resources, principles to applications
inferred← citeshttps://doi.org/10.3389/fimmu.2016.00587openalex-snapshot
Embracing Complexity beyond Systems Medicine: A New Approach to Chronic Immune Disorders
inferred← citeshttps://doi.org/10.3389/fnimg.2024.1455436openalex-snapshot
Inferring neurocognition using artificial intelligence on brain MRIs
inferred← citeshttps://doi.org/10.3389/fphar.2023.1187896openalex-snapshot
Identifying target organ location of Radix Achyranthis Bidentatae: a bioinformatics approach on active compounds and genes
inferred← citeshttps://doi.org/10.3390/genes14010222openalex-snapshot
Evolutionary Landscape of SOX Genes to Inform Genotype-to-Phenotype Relationships
inferred← citeshttps://doi.org/10.3390/ijms18010037openalex-snapshot
Neuroblastoma, a Paradigm for Big Data Science in Pediatric Oncology
inferred← citeshttps://doi.org/10.3390/ijms18020472openalex-snapshot
The Importance of Endophenotypes to Evaluate the Relationship between Genotype and External Phenotype
inferred← citeshttps://doi.org/10.3390/ijns5040040openalex-snapshot
Next Generation Sequencing in Newborn Screening in the United Kingdom National Health Service
inferred← citeshttps://doi.org/10.3390/jpm14060648openalex-snapshot
SwissGenVar: A Platform for Clinical-Grade Interpretation of Genetic Variants to Foster Personalized Healthcare in Switzerland
inferred← citeshttps://doi.org/10.4103/ijmy.ijmy_105_23openalex-snapshot
Bioinformatic Approach for Repurposing Immunomodulatory Drugs for Lepromatous Leprosy
inferred← citeshttps://doi.org/10.5771/9783748927242-114openalex-snapshot
4. Themenbereich genetische Diagnostik: Das humane Genom in der medizinischen Diagnostik
inferred← citeshttps://doi.org/10.6084/m9.figshare.15567120openalex-snapshot
Additional file 1 of VariantStore: an index for large-scale genomic variant search
inferred← citeshttps://doi.org/10.70675/c9668778z4218z4692z908fz449455de3a1eopenalex-snapshot
Integration de multiples approches omiques pour ameliorer la prise en charge des patients atteints de cancer pediatrique
inferred← citeshttps://doi.org/10.70675/e62a0ca5z7722z4c72z9d57z726ae2bc0e42openalex-snapshot
Développement de stratégies de criblage de mutations d'épissage dans des gènes de prédisposition au cancer.
inferred← citeshttps://doi.org/10.7861/clinmedicine.19-1-30openalex-snapshot
The utility of phenomics in diagnosis of inherited metabolic disorders
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