MONDO

Other names: MONDO, Mondo Disease Ontology

Monarch Disease Ontology. A semi-automatically constructed ontology that merges in multiple disease resources to yield a coherent merged ontology.

Webpage:

http://obofoundry.org/ontology/mondo.html

Licence:

Name: Creative Commons Attribution v4.0
URL: https://github.com/monarch-initiative/mondo

Publications:

Publications
More detailed information about this field from each metasource.

The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species
PMID: 27899636
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

https://mondo.monarchinitiative.org/pages/resources/
metasource: Biontology / Bioportal
version: releases/2022-11-01 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/MONDO

The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species PubMed citations: 128.

128 articles citing: The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species

Transcriptional regulatory networks of circulating immune cells in type 1 diabetes: A community knowledgebase. PMID:35832893
Meiotic drive in house mice: mechanisms, consequences, and insights for human biology. PMID:35829972
The heterogeneous pharmacological medical biochemical network PharMeBINet. PMID:35821017
SperoPredictor: An Integrated Machine Learning and Molecular Docking-Based Drug Repurposing Framework With Use Case of COVID-19. PMID:35784208
Deepening the knowledge of rare diseases dependent on angiogenesis through semantic similarity clustering and network analysis. PMID:35731990
DisPhaseDB: An integrative database of diseases related variations in liquid-liquid phase separation proteins. PMID:35685370
Improving medical term embeddings using UMLS Metathesaurus. PMID:35488252
Nationwide comprehensive epidemiological study of rare diseases in Japan using a health insurance claims database. PMID:35346288
The druggable schizophrenia genome: from repurposing opportunities to unexplored drug targets. PMID:35338153
Fission stories: using PomBase to understand Schizosaccharomyces pombe biology. PMID:35100366
The importance of automation in genetic diagnosis: Lessons from analyzing an inherited retinal degeneration cohort with the Mendelian Analysis Toolkit (MATK). PMID:34906470
The Aliment to Bodily Condition knowledgebase (ABCkb): a database connecting plants and human health. PMID:34838100
Network medicine for disease module identification and drug repurposing with the NeDRex platform. PMID:34824199
PHI-base in 2022: a multi-species phenotype database for Pathogen-Host Interactions. PMID:34788826
MoG+: a database of genomic variations across three mouse subspecies for biomedical research. PMID:34782917
Cell type ontologies of the Human Cell Atlas. PMID:34750578
The Rat Genome Database (RGD) facilitates genomic and phenotypic data integration across multiple species for biomedical research. PMID:34741192
Mouse Genome Informatics (MGI): latest news from MGD and GXD. PMID:34698891
Development of the International Classification of Diseases Ontology (ICDO) and its application for COVID-19 diagnostic data analysis. PMID:34663204
An ontology network for Diabetes Mellitus in Mexico. PMID:34625104
Pleiotropy data resource as a primer for investigating co-morbidities/multi-morbidities and their role in disease. PMID:34524473
Catalyzing Knowledge-Driven Discovery in Environmental Health Sciences through a Community-Driven Harmonized Language. PMID:34501574
Evaluating, Filtering and Clustering Genetic Disease Cohorts Based on Human Phenotype Ontology Data with Cohort Analyzer. PMID:34442375
Linking common human diseases to their phenotypes; development of a resource for human phenomics. PMID:34425897
Scaling national and international improvement in virtual gene panel curation via a collaborative approach to discordance resolution. PMID:34329581
Disease ontologies for knowledge graphs. PMID:34289807
The Progenetix oncogenomic resource in 2021. PMID:34272855
Strategies to Uplift Novel Mendelian Gene Discovery for Improved Clinical Outcomes. PMID:34220947
An overview of graph databases and their applications in the biomedical domain. PMID:34003247
Integration of evidence across human and model organism studies: A meeting report. PMID:33893716
Synergizing Mouse and Human Studies to Understand the Heterogeneity of Obesity. PMID:33885739
KnetMiner: a comprehensive approach for supporting evidence-based gene discovery and complex trait analysis across species. PMID:33750020
Detecting Causal Variants in Mendelian Disorders Using Whole-Genome Sequencing. PMID:33606250
Public data sources to support systems toxicology applications. PMID:33604492
The landscape of nutri-informatics: a review of current resources and challenges for integrative nutrition research. PMID:33494105
An empirical meta-analysis of the life sciences linked open data on the web. PMID:33479214
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
MicroPhenoDB Associates Metagenomic Data with Pathogenic Microbes, Microbial Core Genes, and Human Disease Phenotypes. PMID:33418085
Bioinformatics Analysis of Key Genes and Pathways of Cervical Cancer. PMID:33402836
Community Approaches for Integrating Environmental Exposures into Human Models of Disease. PMID:33369481
A Rab escort protein regulates the MAPK pathway that controls filamentous growth in yeast. PMID:33335117
KG-COVID-19: A Framework to Produce Customized Knowledge Graphs for COVID-19 Response. PMID:33196056
An integrative knowledge graph for rare diseases, derived from the Genetic and Rare Diseases Information Center (GARD). PMID:33183351
EpiGraphDB: a database and data mining platform for health data science. PMID:33165574
Pharmacology-informed prediction of the risk posed to fish by mixtures of non-steroidal anti-inflammatory drugs (NSAIDs) in the environment. PMID:33157376
PK-DB: pharmacokinetics database for individualized and stratified computational modeling. PMID:33151297
Alternative genomic diagnoses for individuals with a clinical diagnosis of Dubowitz syndrome. PMID:33098347
The Dark Kinase Knowledgebase: an online compendium of knowledge and experimental results of understudied kinases. PMID:33079988
Integration of anatomy ontology data with protein-protein interaction networks improves the candidate gene prediction accuracy for anatomical entities. PMID:33028186
KG-COVID-19: a framework to produce customized knowledge graphs for COVID-19 response. PMID:32839776
Interpretation of psychiatric genome-wide association studies with multispecies heterogeneous functional genomic data integration. PMID:32791514
Clinical Bioinformatics in Precise Diagnosis of Mitochondrial Disease. PMID:32439066
GlyGen data model and processing workflow. PMID:32324859
Structured reviews for data and knowledge-driven research. PMID:32283553
A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer. PMID:32246132
Wikidata as a knowledge graph for the life sciences. PMID:32180547
Clinical Interpretation of Sequence Variants. PMID:32176464
ncRPheno: a comprehensive database platform for identification and validation of disease related noncoding RNAs. PMID:32122231
Exploring Integrative Analysis Using the BioMedical Evidence Graph. PMID:32097025
Using the electronic health record for genomics research. PMID:32073412
Open Science principles for accelerating trait-based science across the Tree of Life. PMID:32066887
The Deep Genome Project. PMID:32008577
GenoSurf: metadata driven semantic search system for integrated genomic datasets. PMID:31820804
The Alliance of Genome Resources: Building a Modern Data Ecosystem for Model Organism Databases. PMID:31796553
Comparative analysis of functional assay evidence use by ClinGen Variant Curation Expert Panels. PMID:31783775
Representing glycophenotypes: semantic unification of glycobiology resources for disease discovery. PMID:31735951
The assessment of efficient representation of drug features using deep learning for drug repositioning. PMID:31726977
Gold-standard ontology-based anatomical annotation in the CRAFT Corpus. PMID:31725864
The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species. PMID:31701156
Enabling semantic queries across federated bioinformatics databases. PMID:31697362
Mouse Phenome Database: a data repository and analysis suite for curated primary mouse phenotype data. PMID:31696236
GWAS Central: a comprehensive resource for the discovery and comparison of genotype and phenotype data from genome-wide association studies. PMID:31612961
VarSite: Disease variants and protein structure. PMID:31606900
Alliance of Genome Resources Portal: unified model organism research platform. PMID:31552413
Gephebase, a database of genotype-phenotype relationships for natural and domesticated variation in Eukaryotes. PMID:31544935
Using MARRVEL v1.2 for Bioinformatics Analysis of Human Genes and Variant Pathogenicity. PMID:31524990
In Vivo Functional Study of Disease-associated Rare Human Variants Using Drosophila. PMID:31498321
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
Closing the 'phenotype gap' in precision medicine: improving what we measure to understand complex disease mechanisms. PMID:31428846
A genetics-led approach defines the drug target landscape of 30 immune-related traits. PMID:31253980
The Global academic research organization network: Data sharing to cure diseases and enable learning health systems. PMID:31245596
Predicting instances of pathway ontology classes for pathway integration. PMID:31196182
High-Diversity Mouse Populations for Complex Traits. PMID:31133439
New models for human disease from the International Mouse Phenotyping Consortium. PMID:31127358
Doc2Hpo: a web application for efficient and accurate HPO concept curation. PMID:31106327
Intellectual disability and autism spectrum disorders 'on the fly': insights from Drosophila. PMID:31088981
Ten quick tips for biocuration. PMID:31048830
An analysis and metric of reusable data licensing practices for biomedical resources. PMID:30917137
From Big Data to Precision Medicine. PMID:30881956
DDOT: A Swiss Army Knife for Investigating Data-Driven Biological Ontologies. PMID:30878356
Ontology based text mining of gene-phenotype associations: application to candidate gene prediction. PMID:30809638
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 Importance of Biologic Knowledge and Gene Expression Context for Genomic Data Interpretation. PMID:30619486
Computational aspects underlying genome to phenome analysis in plants. PMID:30500991
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
Gene's hubs in retinal diseases: A retinal disease network. PMID:30417144
Mapping Molecular Datasets Back to the Brain Regions They are Extracted from: Remembering the Native Countries of Hypothalamic Expatriates and Refugees. PMID:30334222
ClinGen advancing genomic data-sharing standards as a GA4GH driver project. PMID:30311379
Classification, Ontology, and Precision Medicine. PMID:30304648
Knowledge-based biomedical Data Science. PMID:30294517
Uncovering new disease indications for G-protein coupled receptors and their endogenous ligands. PMID:30285606
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
Computational resources associating diseases with genotypes, phenotypes and exposures. PMID:30102366
Creating a Structured AOP Knowledgebase via Ontology-Based Annotations. PMID:30057931
Deep Phenotyping on Electronic Health Records Facilitates Genetic Diagnosis by Clinical Exomes. PMID:29961570
GNOMICS: A one-stop shop for biomedical and genomic data. PMID:29888054
Chemical-Induced Phenotypes at CTD Help Inform the Predisease State and Construct Adverse Outcome Pathways. PMID:29846728
Plain-language medical vocabulary for precision diagnosis. PMID:29632381
High-throughput mouse phenomics for characterizing mammalian gene function. PMID:29626206
Unexplored therapeutic opportunities in the human genome. PMID:29472638
Text-based phenotypic profiles incorporating biochemical phenotypes of inborn errors of metabolism improve phenomics-based diagnosis. PMID:29340838
Integrating phenotype ontologies with PhenomeNET. PMID:29258588
Mouse Phenome Database: an integrative database and analysis suite for curated empirical phenotype data from laboratory mice. PMID:29136208
Towards precision medicine in Alzheimer's disease: deciphering genetic data to establish informative biomarkers. PMID:28944295
Systematic integration of biomedical knowledge prioritizes drugs for repurposing. PMID:28936969
Gene2Function: An Integrated Online Resource for Gene Function Discovery. PMID:28663344
Knowledge Discovery in Biological Databases for Revealing Candidate Genes Linked to Complex Phenotypes. PMID:28609292
Defining Disease, Diagnosis, and Translational Medicine within a Homeostatic Perturbation Paradigm: The National Institutes of Health Undiagnosed Diseases Program Experience. PMID:28603714
Naming CRISPR alleles: endonuclease-mediated mutation nomenclature across species. PMID:28589392
MARRVEL: Integration of Human and Model Organism Genetic Resources to Facilitate Functional Annotation of the Human Genome. PMID:28502612
The anatomy of phenotype ontologies: principles, properties and applications. PMID:28387809
The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. PMID:28053160
https://mondo.monarchinitiative.org/pages/resources/

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