FAIRsharing.8b6wfq; Last edited: Aug. 5, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:10 p.m.

DO
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:44.576292

disease_ontology
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:44.576292

Other names: DOID, DO, disease_ontology

The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts. Releases: https://github.com/DiseaseOntology/HumanDiseaseOntology/releases

Webpage:

http://www.disease-ontology.org

Licence:

Name: Creative Commons Universal v1.0 - no copyright
URL: http://www.disease-ontology.org/resources/

Publications:

Publications
More detailed information about this field from each metasource.

Disease Ontology: a backbone for disease semantic integration
PMID: 22080554
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

metasource: Fairsharing.org
version: FAIRsharing.org: DOID; Disease Ontology; DOI: https://doi.org/10.25504/FAIRsharing.8b6wfq; Last edited: Aug. 5, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:10 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:44.576292

Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data
PMID: 25348409
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

metasource: Fairsharing.org
version: FAIRsharing.org: DOID; Disease Ontology; DOI: https://doi.org/10.25504/FAIRsharing.8b6wfq; Last edited: Aug. 5, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:10 p.m.

From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations
PMID: 19478018
metasource: Fairsharing.org
version: FAIRsharing.org: DOID; Disease Ontology; DOI: https://doi.org/10.25504/FAIRsharing.8b6wfq; Last edited: Aug. 5, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:10 p.m.

http://dx.doi.org/10.1093/nar/gku1011
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

Disease Ontology: a backbone for disease semantic integration PubMed citations: 308.

308 articles citing: Disease Ontology: a backbone for disease semantic integration

PheNominal: an EHR-integrated web application for structured deep phenotyping at the point of care. PMID:35902925
The Core Human Microbiome: Does It Exist and How Can We Find It? A Critical Review of the Concept. PMID:35889831
Prediction of circRNA-Disease Associations Based on the Combination of Multi-Head Graph Attention Network and Graph Convolutional Network. PMID:35883487
Transcriptomic and proteomic retinal pigment epithelium signatures of age-related macular degeneration. PMID:35882847
Omics-based integrated analysis identified IKZF2 as a biomarker associated with lupus nephritis. PMID:35688845
AnthraxKP: a knowledge graph-based, Anthrax Knowledge Portal mined from biomedical literature. PMID:35653350
A Simple Standard for Sharing Ontological Mappings (SSSOM). PMID:35616100
A molecular view of amyotrophic lateral sclerosis through the lens of interaction network modules. PMID:35576218
Transcriptome Analysis of Monocytes and Fibroblasts Provides Insights Into the Molecular Features of Periodontal Ehlers-Danlos Syndrome. PMID:35571048
NCPCDA: network consistency projection for circRNA-disease association prediction. PMID:35529153
Upregulated of ANXA3, SORL1, and Neutrophils May Be Key Factors in the Progressionof Ankylosing Spondylitis. PMID:35464477
MeFSAT: a curated natural product database specific to secondary metabolites of medicinal fungi. PMID:35424258
Combining biomedical knowledge graphs and text to improve predictions for drug-target interactions and drug-indications. PMID:35402106
Ontology-Based Classification and Analysis of Adverse Events Associated With the Usage of Chloroquine and Hydroxychloroquine. PMID:35401219
Whole-genome sequencing reveals host factors underlying critical COVID-19. PMID:35255492
PSINDB: the postsynaptic protein-protein interaction database. PMID:35234850
An ensemble approach for healthcare application and diagnosis using natural language processing. PMID:35069926
Effects of Negation and Uncertainty Stratification on Text-Derived Patient Profile Similarity. PMID:34939069
Construction of the cervical cancer common terminology for promoting semantic interoperability and utilization of Chinese clinical data. PMID:34789237
Biomedical Ontologies to Guide AI Development in Radiology. PMID:34724143
BrainBase: a curated knowledgebase for brain diseases. PMID:34718720
Development of the International Classification of Diseases Ontology (ICDO) and its application for COVID-19 diagnostic data analysis. PMID:34663204
NCATS Inxight Drugs: a comprehensive and curated portal for translational research. PMID:34648031
TSMDA: Target and symptom-based computational model for miRNA-disease-association prediction. PMID:34631283
An ontology network for Diabetes Mellitus in Mexico. PMID:34625104
Multi-faceted semantic clustering with text-derived phenotypes. PMID:34600327
Gene Expression Nebulas (GEN): a comprehensive data portal integrating transcriptomic profiles across multiple species at both bulk and single-cell levels. PMID:34591957
An automated method to enrich consumer health vocabularies using GloVe word embeddings and an auxiliary lexical resource. PMID:34458573
Ten simple rules for creating reusable pathway models for computational analysis and visualization. PMID:34411100
Elucidation of dynamic microRNA regulations in cancer progression using integrative machine learning. PMID:34373890
Mining a stroke knowledge graph from literature. PMID:34325669
Representing a Heterogeneous Pharmaceutical Knowledge-Graph with Textual Information. PMID:34278204
Development and application of the ocular immune-mediated inflammatory diseases ontology enhanced with synonyms from online patient support forum conversation. PMID:34139439
PhenCards: a data resource linking human phenotype information to biomedical knowledge. PMID:34034817
An overview of graph databases and their applications in the biomedical domain. PMID:34003247
System biology and bioinformatics pipeline to identify comorbidities risk association: Neurodegenerative disorder case study. PMID:33956862
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
Ontology-driven weak supervision for clinical entity classification in electronic health records. PMID:33795682
Modular genome-wide gene expression architecture shared by early traits of osteoporosis and atherosclerosis in the Young Finns Study. PMID:33782480
Named Data Networking for Genomics Data Management and Integrated Workflows. PMID:33748749
The glycoconjugate ontology (GlycoCoO) for standardizing the annotation of glycoconjugate data and its application. PMID:33677548
InContext: curation of medical context for drug indications. PMID:33579375
Diseasome and comorbidities complexities of SARS-CoV-2 infection with common malignant diseases. PMID:33539530
Developmental cell programs are co-opted in inflammatory skin disease. PMID:33479125
Identifying diseases that cause psychological trauma and social avoidance by GCN-Xgboost. PMID:33323103
Towards semantic interoperability: finding and repairing hidden contradictions in biomedical ontologies. PMID:33319712
Analysis of readability and structural accuracy in SNOMED CT. PMID:33319711
HERB: a high-throughput experiment- and reference-guided database of traditional Chinese medicine. PMID:33264402
DEEPScreen: high performance drug-target interaction prediction with convolutional neural networks using 2-D structural compound representations. PMID:33209251
Inferring Potential CircRNA-Disease Associations via Deep Autoencoder-Based Classification. PMID:33156515
TCRD and Pharos 2021: mining the human proteome for disease biology. PMID:33156327
Informing epidemic (research) responses in a timely fashion by knowledge management - a Zika virus use case. PMID:33148605
Distribution of disease-causing germline mutations in coiled-coils implies an important role of their N-terminal region. PMID:33060664
Creating Neuroscientific Knowledge Organization System Based on Word Representation and Agglomerative Clustering Algorithm. PMID:33013345
SC2disease: a manually curated database of single-cell transcriptome for human diseases. PMID:33010177
High-throughput small molecule screening reveals Nrf2-dependent and -independent pathways of cellular stress resistance. PMID:33008901
Finding semantic patterns in omics data using concept rule learning with an ontology-based refinement operator. PMID:32905086
The effect of compound kushen injection on cancer cells: Integrated identification of candidate molecular mechanisms. PMID:32730293
Network-principled deep generative models for designing drug combinations as graph sets. PMID:32657357
Ontology-driven aspect-based sentiment analysis classification: An infodemiological case study regarding infectious diseases in Latin America. PMID:32572291
pyMeSHSim: an integrative python package for biomedical named entity recognition, normalization, and comparison of MeSH terms. PMID:32552728
Aggregation and analysis of indication-symptom relationships for drugs approved in the USA. PMID:32495081
PRISM: A Platform for Imaging in Precision Medicine. PMID:32479186
BEAVR: a browser-based tool for the exploration and visualization of RNA-seq data. PMID:32471392
A Literature Review of Gene Function Prediction by Modeling Gene Ontology. PMID:32391061
Applying knowledge-driven mechanistic inference to toxicogenomics. PMID:32387679
BioHackathon 2015: Semantics of data for life sciences and reproducible research. PMID:32308977
Prediction of circRNA-disease associations based on inductive matrix completion. PMID:32241268
MEDICASCY: A Machine Learning Approach for Predicting Small-Molecule Drug Side Effects, Indications, Efficacy, and Modes of Action. PMID:32237745
Supervised learning is an accurate method for network-based gene classification. PMID:32129827
Pathogenic Gene Prediction Algorithm Based on Heterogeneous Information Fusion. PMID:32117433
DISNET: a framework for extracting phenotypic disease information from public sources. PMID:32110491
Discovering the genes mediating the interactions between chronic respiratory diseases in the human interactome. PMID:32041952
Combining lexical and context features for automatic ontology extension. PMID:31931870
Text-mining clinically relevant cancer biomarkers for curation into the CIViC database. PMID:31796060
The Immune Epitope Database and Analysis Resource Program 2003-2018: reflections and outlook. PMID:31761977
Identifying Alzheimer's disease-related proteins by LRRGD. PMID:31760934
Discovery of disease- and drug-specific pathways through community structures of a literature network. PMID:31738408
Dissecting the Shared and Context-Dependent Pathways Mediated by the p140Cap Adaptor Protein in Cancer and in Neurons. PMID:31681758
Computational Methods for Identifying Similar Diseases. PMID:31678735
miR2Diabetes: A Literature-Curated Database of microRNA Expression Patterns, in Diabetic Microvascular Complications. PMID:31601051
Ontological and Non-Ontological Resources for Associating Medical Dictionary for Regulatory Activities Terms to SNOMED Clinical Terms With Semantic Properties. PMID:31551780
SKF-LDA: Similarity Kernel Fusion for Predicting lncRNA-Disease Association. PMID:31514111
FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration. PMID:31304272
Integrating biomedical research and electronic health records to create knowledge-based biologically meaningful machine-readable embeddings. PMID:31292438
Prioritizing target-disease associations with novel safety and efficacy scoring methods. PMID:31285471
Disease gene prediction for molecularly uncharacterized diseases. PMID:31276496
The cell line ontology-based representation, integration and analysis of cell lines used in China. PMID:31272367
Enhancing ontology-driven diagnostic reasoning with a symptom-dependency-aware Naïve Bayes classifier. PMID:31196129
A Novel Method for Predicting Disease-Associated LncRNA-MiRNA Pairs Based on the Higher-Order Orthogonal Iteration. PMID:31191710
An Effective Method to Measure Disease Similarity Using Gene and Phenotype Associations. PMID:31164903
Population Levels Assessment of the Distribution of Disease-Associated Variants With Emphasis on Armenians - A Machine Learning Approach. PMID:31105750
ODAE: Ontology-based systematic representation and analysis of drug adverse events and its usage in study of adverse events given different patient age and disease conditions. PMID:31074377
GeneSurrounder: network-based identification of disease genes in expression data. PMID:31060502
The multiplex network of human diseases. PMID:31044086
Technological Innovations in Disease Management: Text Mining US Patent Data From 1995 to 2017. PMID:31038462
The Transcriptomic Toolbox: Resources for Interpreting Large Gene Expression Data within a Precision Medicine Context for Metabolic Disease Atherosclerosis. PMID:31032818
Seeing the whole picture: integrated pre-surgery reports with PreOptique. PMID:30832727
CSgator: an integrated web platform for compound set analysis. PMID:30830479
Mining Disease-Symptom Relation from Massive Biomedical Literature and Its Application in Severe Disease Diagnosis. PMID:30815154
How Sustainable are Biomedical Ontologies? PMID:30815087
Prediction of lncRNA-disease associations by integrating diverse heterogeneous information sources with RWR algorithm and positive pointwise mutual information. PMID:30782113
Conserved Disease Modules Extracted From Multilayer Heterogeneous Disease and Gene Networks for Understanding Disease Mechanisms and Predicting Disease Treatments. PMID:30713550
Utility of the JAX Clinical Knowledgebase in capture and assessment of complex genomic cancer data. PMID:30675517
Restructured GEO: restructuring Gene Expression Omnibus metadata for genome dynamics analysis. PMID:30649296
Integrating ontologies of human diseases, phenotypes, and radiological diagnosis. PMID:30624645
Global analysis of N6-methyladenosine functions and its disease association using deep learning and network-based methods. PMID:30601803
From Matrices to Knowledge: Using Semantic Networks to Annotate the Connectome. PMID:30581382
Early-onset inflammatory bowel disease as a model disease to identify key regulators of immune homeostasis mechanisms. PMID:30565237
Variant information systems for precision oncology. PMID:30463544
The Pathogenesis of Atherosclerosis Based on Human Signaling Networks and Stem Cell Expression Data. PMID:30416382
Arena-Idb: a platform to build human non-coding RNA interaction networks. PMID:30367585
From Affective Science to Psychiatric Disorder: Ontology as a Semantic Bridge. PMID:30349491
Linked open data-based framework for automatic biomedical ontology generation. PMID:30200874
The CAIRR Pipeline for Submitting Standards-Compliant B and T Cell Receptor Repertoire Sequencing Studies to the National Center for Biotechnology Information Repositories. PMID:30166985
Glycomics@ExPASy: Bridging the Gap. PMID:30097532
EAPB: entropy-aware path-based metric for ontology quality. PMID:30097014
Regional Diversity in the Postsynaptic Proteome of the Mouse Brain. PMID:30071621
HDncRNA: a comprehensive database of non-coding RNAs associated with heart diseases. PMID:30053237
CEDAR OnDemand: a browser extension to generate ontology-based scientific metadata. PMID:30012108
DEXTER: Disease-Expression Relation Extraction from Text. PMID:29860481
Towards precision informatics of pharmacovigilance: OAE-CTCAE mapping and OAE-based representation and analysis of adverse events in patients treated with cancer drugs. PMID:29854250
Leveraging Collaborative Filtering to Accelerate Rare Disease Diagnosis. PMID:29854225
Fast and Accurate Metadata Authoring Using Ontology-Based Recommendations. PMID:29854196
A Novel Model for Predicting Associations between Diseases and LncRNA-miRNA Pairs Based on a Newly Constructed Bipartite Network. PMID:29853986
Fast-Evolving Human-Specific Neural Enhancers Are Associated with Aging-Related Diseases. PMID:29792826
Using WormBase: A Genome Biology Resource for Caenorhabditis elegans and Related Nematodes. PMID:29761466
Using ZFIN: Data Types, Organization, and Retrieval. PMID:29761463
Extending the DIDEO ontology to include entities from the natural product drug interaction domain of discourse. PMID:29743102
AllerGAtlas 1.0: a human allergy-related genes database. PMID:29688358
Identification of errors in the IEDB using ontologies. PMID:29688357
Disease Ontology: improving and unifying disease annotations across species. PMID:29590633
Where to search top-K biomedical ontologies? PMID:29579141
IMPPAT: A curated database of Indian Medicinal Plants, Phytochemistry And Therapeutics. PMID:29531263
Loss and gain of N-linked glycosylation sequons due to single-nucleotide variation in cancer. PMID:29531238
A comprehensive and quantitative comparison of text-mining in 15 million full-text articles versus their corresponding abstracts. PMID:29447159
A phenotype centric benchmark of variant prioritisation tools. PMID:29423277
Systematic identification of latent disease-gene associations from PubMed articles. PMID:29373609
Tackling the challenges of matching biomedical ontologies. PMID:29335022
Systematic target function annotation of human transcription factors. PMID:29325558
Ontological representation, integration, and analysis of LINCS cell line cells and their cellular responses. PMID:29322930
DisSetSim: an online system for calculating similarity between disease sets. PMID:29297411
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
Integrating phenotype ontologies with PhenomeNET. PMID:29258588
NutriChem 2.0: exploring the effect of plant-based foods on human health and drug efficacy. PMID:29220436
Learning bundled care opportunities from electronic medical records. PMID:29174994
Chromosome preference of disease genes and vectorization for the prediction of non-coding disease genes. PMID:29108274
LiverWiki: a wiki-based database for human liver. PMID:29029599
Knowledge Management Framework for Emerging Infectious Diseases Preparedness and Response: Design and Development of Public Health Document Ontology. PMID:29021130
A novel network analysis approach reveals DNA damage, oxidative stress and calcium/cAMP homeostasis-associated biomarkers in frontotemporal dementia. PMID:29020091
BRWLDA: bi-random walks for predicting lncRNA-disease associations. PMID:28947982
Systematic integration of biomedical knowledge prioritizes drugs for repurposing. PMID:28936969
Fish Ontology framework for taxonomy-based fish recognition. PMID:28929028
Precision annotation of digital samples in NCBI's gene expression omnibus. PMID:28925997
Search Datasets in Literature: A Case Study of GWAS. PMID:28815103
An extensible framework and database of infectious disease for biosurveillance. PMID:28784113
Towards a more molecular taxonomy of disease. PMID:28750648
Synaptic Interactome Mining Reveals p140Cap as a New Hub for PSD Proteins Involved in Psychiatric and Neurological Disorders. PMID:28713243
Context Is Everything: Harmonization of Critical Food Microbiology Descriptors and Metadata for Improved Food Safety and Surveillance. PMID:28694792
Evaluating phecodes, clinical classification software, and ICD-9-CM codes for phenome-wide association studies in the electronic health record. PMID:28686612
Classification and analysis of a large collection of in vivo bioassay descriptions. PMID:28678787
Bioinformatics analysis of transcription profiling of solid pseudopapillary neoplasm of the pancreas. PMID:28627654
HGPEC: a Cytoscape app for prediction of novel disease-gene and disease-disease associations and evidence collection based on a random walk on heterogeneous network. PMID:28619054
Integration of over 9,000 mass spectrometry experiments builds a global map of human protein complexes. PMID:28596423
NCBO Ontology Recommender 2.0: an enhanced approach for biomedical ontology recommendation. PMID:28592275
A disease similarity matrix based on the uniqueness of shared genes. PMID:28589854
Recent advances in predicting gene-disease associations. PMID:28529714
Use of Biomedical Ontologies for Integration of Biological Knowledge for Learning and Prediction of Adverse Drug Reactions. PMID:28469412
Use of Graph Database for the Integration of Heterogeneous Biological Data. PMID:28416946
In silico prediction of lncRNA function using tissue specific and evolutionary conserved expression. PMID:28361701
The druggable genome and support for target identification and validation in drug development. PMID:28356508
Cross disease analysis of co-functional microRNA pairs on a reconstructed network of disease-gene-microRNA tripartite. PMID:28340554
Medical Subject Heading (MeSH) annotations illuminate maize genetics and evolution. PMID:28250803
Predicting disease-related genes using integrated biomedical networks. PMID:28198675
Utilizing somatic mutation data from numerous studies for cancer research: proof of concept and applications. PMID:28092680
Construction of an miRNA-regulated drug-pathway network reveals drug repurposing candidates for myasthenia gravis. PMID:28075449
Developing the Quantitative Histopathology Image Ontology (QHIO): A case study using the hot spot detection problem. PMID:28003147
Identification of disease comorbidity through hidden molecular mechanisms. PMID:27991583
XGR software for enhanced interpretation of genomic summary data, illustrated by application to immunological traits. PMID:27964755
Microbial phenomics information extractor (MicroPIE): a natural language processing tool for the automated acquisition of prokaryotic phenotypic characters from text sources. PMID:27955641
AAgAtlas 1.0: a human autoantigen database. PMID:27924021
Pharos: Collating protein information to shed light on the druggable genome. PMID:27903890
Knowledge Representation and Management: a Linked Data Perspective. PMID:27830248
Systematic Analysis of Drug Targets Confirms Expression in Disease-Relevant Tissues. PMID:27824084
The Pre-Eclampsia Ontology: A Disease Ontology Representing the Domain Knowledge Specific to Pre-Eclampsia. PMID:27788142
TrhOnt: building an ontology to assist rehabilitation processes. PMID:27716359
OAHG: an integrated resource for annotating human genes with multi-level ontologies. PMID:27703231
Mapping Phenotypic Information in Heterogeneous Textual Sources to a Domain-Specific Terminological Resource. PMID:27643689
Integrated Analysis of DNA Methylation and mRNA Expression Profiles Data to Identify Key Genes in Lung Adenocarcinoma. PMID:27610375
The Current Landscape of Genetic Testing in Cardiovascular Malformations: Opportunities and Challenges. PMID:27504451
Gene-Disease Interaction Retrieval from Multiple Sources: A Network Based Method. PMID:27478829
DisSim: an online system for exploring significant similar diseases and exhibiting potential therapeutic drugs. PMID:27457921
A method for exploring implicit concept relatedness in biomedical knowledge network. PMID:27454167
BLAT2DOLite: An Online System for Identifying Significant Relationships between Genetic Sequences and Diseases. PMID:27315278
An integer programming framework for inferring disease complexes from network data. PMID:27307626
Comparative analyses of population-scale phenomic data in electronic medical records reveal race-specific disease networks. PMID:27307606
AuDis: an automatic CRF-enhanced disease normalization in biomedical text. PMID:27278815
HITSZ_CDR: an end-to-end chemical and disease relation extraction system for BioCreative V. PMID:27270713
Identifying functional cancer-specific miRNA-mRNA interactions in testicular germ cell tumor. PMID:27235586
Reactome from a WikiPathways Perspective. PMID:27203685
Identification of polycystic ovary syndrome potential drug targets based on pathobiological similarity in the protein-protein interaction network. PMID:27191267
BioSharing: curated and crowd-sourced metadata standards, databases and data policies in the life sciences. PMID:27189610
Argo: enabling the development of bespoke workflows and services for disease annotation. PMID:27189607
Ontology-based annotations and semantic relations in large-scale (epi)genomics data. PMID:27142216
VICO: Ontology-based representation and integrative analysis of Vaccination Informed Consent forms. PMID:27099700
In silico methods for drug repurposing and pharmacology. PMID:27080087
Extending gene ontology in the context of extracellular RNA and vesicle communication. PMID:27076901
MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions. PMID:27076900
Efficient chemical-disease identification and relationship extraction using Wikipedia to improve recall. PMID:27060160
Linking MedDRA(®)-Coded Clinical Phenotypes to Biological Mechanisms by the Ontology of Adverse Events: A Pilot Study on Tyrosine Kinase Inhibitors. PMID:27003817
A method for the development of disease-specific reference standards vocabularies from textual biomedical literature resources. PMID:26971304
Ten Simple Rules for Selecting a Bio-ontology. PMID:26867217
Consent Codes: Upholding Standard Data Use Conditions. PMID:26796797
Network-based analysis of genetic variants associated with hippocampal volume in Alzheimer's disease: a study of ADNI cohorts. PMID:26788126
Text Mining the History of Medicine. PMID:26734936
Dealing with the Data Deluge: Handling the Multitude Of Chemical Biology Data Sources. PMID:26609498
PhenoMiner: from text to a database of phenotypes associated with OMIM diseases. PMID:26507285
A Molecular-Level Landscape of Diet-Gut Microbiome Interactions: Toward Dietary Interventions Targeting Bacterial Genes. PMID:26507230
Methods for biological data integration: perspectives and challenges. PMID:26490630
Genome-Wide Detection and Analysis of Multifunctional Genes. PMID:26436655
My Corporis Fabrica Embryo: An ontology-based 3D spatio-temporal modeling of human embryo development. PMID:26413258
Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases. PMID:26362267
Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies. PMID:26320941
Integrating Multiple On-line Knowledge Bases for Disease-Lab Test Relation Extraction. PMID:26306271
A knowledge-based, automated method for phenotyping in the EHR using only clinical pathology reports. PMID:26306239
Integrated analysis of numerous heterogeneous gene expression profiles for detecting robust disease-specific biomarkers and proposing drug targets. PMID:26261215
BioModels: Content, Features, Functionality, and Use. PMID:26225232
Best behaviour? Ontologies and the formal description of animal behaviour. PMID:26215546
Phenolyzer: phenotype-based prioritization of candidate genes for human diseases. PMID:26192085
Heterogeneous Network Edge Prediction: A Data Integration Approach to Prioritize Disease-Associated Genes. PMID:26158728
Relationships between predicted moonlighting proteins, human diseases, and comorbidities from a network perspective. PMID:26157390
The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease. PMID:26119816
The Disease Ontology: fostering interoperability between biological and clinical human disease-related data. PMID:26093607
Pathway-Dependent Effectiveness of Network Algorithms for Gene Prioritization. PMID:26091506
TRRUST: a reference database of human transcriptional regulatory interactions. PMID:26066708
DeCoaD: determining correlations among diseases using protein interaction networks. PMID:26047952
Network-based prediction and knowledge mining of disease genes. PMID:26043920
Towards drug repositioning: a unified computational framework for integrating multiple aspects of drug similarity and disease similarity. PMID:25954437
Capturing domain knowledge from multiple sources: the rare bone disorders use case. PMID:25926964
Canadian Open Genetics Repository (COGR): a unified clinical genomics database as a community resource for standardising and sharing genetic interpretations. PMID:25904639
MeSH ORA framework: R/Bioconductor packages to support MeSH over-representation analysis. PMID:25887539
DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes. PMID:25877637
BioXpress: an integrated RNA-seq-derived gene expression database for pan-cancer analysis. PMID:25819073
Supporting the annotation of chronic obstructive pulmonary disease (COPD) phenotypes with text mining workflows. PMID:25789153
HPOSim: an R package for phenotypic similarity measure and enrichment analysis based on the human phenotype ontology. PMID:25664462
An integrative pipeline for multi-modal discovery of disease relationships. PMID:25592600
POEAS: Automated Plant Phenomic Analysis Using Plant Ontology. PMID:25574136
Network-based association of hypoxia-responsive genes with cardiovascular diseases. PMID:25530704
Deciphering miRNA transcription factor feed-forward loops to identify drug repurposing candidates for cystic fibrosis. PMID:25484921
The BioGRID interaction database: 2015 update. PMID:25428363
Text mining in cancer gene and pathway prioritization. PMID:25392685
Relating diseases by integrating gene associations and information flow through protein interaction network. PMID:25360770
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
The immune epitope database (IEDB) 3.0. PMID:25300482
Large-scale modeling of condition-specific gene regulatory networks by information integration and inference. PMID:25294834
The role of the interactome in the maintenance of deleterious variability in human populations. PMID:25261458
Human germline and pan-cancer variomes and their distinct functional profiles. PMID:25232094
Organizing knowledge to enable personalization of medicine in cancer. PMID:25222080
Sequential transcriptional changes dictate safe and effective antigen-specific immunotherapy. PMID:25182274
Semantic Web repositories for genomics data using the eXframe platform. PMID:25093072
comoR: a software for disease comorbidity risk assessment. PMID:25045465
Large scale analysis of phenotype-pathway relationships based on GWAS results. PMID:25007247
Processing biological literature with customizable Web services supporting interoperable formats. PMID:25006225
Genome-wide identification and characterization of fixed human-specific regulatory regions. PMID:24995867
Bridging islands of information to establish an integrated knowledge base of drugs and health outcomes of interest. PMID:24985530
Computational prediction of disease microRNAs in domestic animals. PMID:24970281
Lynx web services for annotations and systems analysis of multi-gene disorders. PMID:24948611
An ontological modeling approach for abnormal states and its application in the medical domain. PMID:24944781
SemFunSim: a new method for measuring disease similarity by integrating semantic and gene functional association. PMID:24932637
Modelling human protein interaction networks as metric spaces has potential in disease research and drug target discovery. PMID:24929653
Egas: a collaborative and interactive document curation platform. PMID:24923820
Event-based text mining for biology and functional genomics. PMID:24907365
OWL reasoning framework over big biological knowledge network. PMID:24877076
Phevor combines multiple biomedical ontologies for accurate identification of disease-causing alleles in single individuals and small nuclear families. PMID:24702956
Thematic series on biomedical ontologies in JBMS: challenges and new directions. PMID:24602198
The epidemiology ontology: an ontology for the semantic annotation of epidemiological resources. PMID:24438387
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
The neurological disease ontology. PMID:24314207
Protein-driven inference of miRNA-disease associations. PMID:24273243
Lynx: a database and knowledge extraction engine for integrative medicine. PMID:24270788
The Reactome pathway knowledgebase. PMID:24243840
Discovering disease-disease associations by fusing systems-level molecular data. PMID:24232732
The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. PMID:24217912
Annotating cancer variants and anti-cancer therapeutics in reactome. PMID:24213504
Experimental design-based functional mining and characterization of high-throughput sequencing data in the sequence read archive. PMID:24167589
SIDD: a semantically integrated database towards a global view of human disease. PMID:24146757
Are graph databases ready for bioinformatics? PMID:24135261
SurvExpress: an online biomarker validation tool and database for cancer gene expression data using survival analysis. PMID:24066126
The mouse pathology ontology, MPATH; structure and applications. PMID:24033988
DNorm: disease name normalization with pairwise learning to rank. PMID:23969135
Towards precision medicine: advances in computational approaches for the analysis of human variants. PMID:23962656
Dizeez: an online game for human gene-disease annotation. PMID:23951102
Quantitative imaging biomarker ontology (QIBO) for knowledge representation of biomedical imaging biomarkers. PMID:23589184
MalaCards: an integrated compendium for diseases and their annotation. PMID:23584832
Neurocarta: aggregating and sharing disease-gene relations for the neurosciences. PMID:23442263
A framework for annotating human genome in disease context. PMID:23251346
The Disease and Gene Annotations (DGA): an annotation resource for human disease. PMID:23197658
DcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more. PMID:23161684
Text mining in the biocuration workflow: applications for literature curation at WormBase, dictyBase and TAIR. PMID:23160413
The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data. PMID:22961259
Nanoinformatics: a new area of research in nanomedicine. PMID:22866003
Gemma: a resource for the reuse, sharing and meta-analysis of expression profiling data. PMID:22782548
Accelerating discovery for complex neurological and behavioral disorders through systems genetics and integrative genomics in the laboratory mouse. PMID:22422471
Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data PubMed citations: 247.

247 articles citing: Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data

DES-Amyloidoses "Amyloidoses through the looking-glass": A knowledgebase developed for exploring and linking information related to human amyloid-related diseases. PMID:35877764
From drug repositioning to target repositioning: prediction of therapeutic targets using genetically perturbed transcriptomic signatures. PMID:35758779
A molecular view of amyotrophic lateral sclerosis through the lens of interaction network modules. PMID:35576218
Transcriptomic Analysis of Fumarate Compounds Identifies Unique Effects of Isosorbide Di-(Methyl Fumarate) on NRF2, NF-kappaB and IRF1 Pathway Genes. PMID:35455458
M2PP: a novel computational model for predicting drug-targeted pathogenic proteins. PMID:34983358
A network-based method for predicting disease-associated enhancers. PMID:34879086
An Overview of Biomedical Ontologies for Pandemics and Infectious Diseases Representation. PMID:34868401
The reactome pathway knowledgebase 2022. PMID:34788843
Network-driven analysis of human-Plasmodium falciparum interactome: processes for malaria drug discovery and extracting in silico targets. PMID:34702263
Development of the International Classification of Diseases Ontology (ICDO) and its application for COVID-19 diagnostic data analysis. PMID:34663204
Genetic Prioritization, Therapeutic Repositioning and Cross-Disease Comparisons Reveal Inflammatory Targets Tractable for Kidney Stone Disease. PMID:34489936
Web tools to perform long non-coding RNAs analysis in oncology research. PMID:34296748
DES-Tcell is a knowledgebase for exploring immunology-related literature. PMID:34253812
Advancing clinical genomics and precision medicine with GVViZ: FAIR bioinformatics platform for variable gene-disease annotation, visualization, and expression analysis. PMID:34174938
Precision omics data integration and analysis with interoperable ontologies and their application for COVID-19 research. PMID:34159360
emiRIT: a text-mining-based resource for microRNA information. PMID:34048547
Lantern: an integrative repository of functional annotations for lncRNAs in the human genome. PMID:34039271
Osteocyte transcriptome mapping identifies a molecular landscape controlling skeletal homeostasis and susceptibility to skeletal disease. PMID:33953184
Network-Based Analysis of Fatal Comorbidities of COVID-19 and Potential Therapeutics. PMID:33891554
Dietary Habit Is Associated with Depression and Intelligence: An Observational and Genome-Wide Environmental Interaction Analysis in the UK Biobank Cohort. PMID:33807197
Cardiovascular informatics: building a bridge to data harmony. PMID:33751044
The similarity of inherited diseases (I): clinical similarity within the phenotypic series. PMID:33622316
CircR2Cancer: a manually curated database of associations between circRNAs and cancers. PMID:33181824
PK-DB: pharmacokinetics database for individualized and stratified computational modeling. PMID:33151297
Integration of anatomy ontology data with protein-protein interaction networks improves the candidate gene prediction accuracy for anatomical entities. PMID:33028186
The similarity of inherited diseases (II): clinical and biological similarity between the phenotypic series. PMID:32972400
Modelling kidney disease using ontology: insights from the Kidney Precision Medicine Project. PMID:32939051
MosaicBase: A Knowledgebase of Postzygotic Mosaic Variants in Noncancer Disease-related and Healthy Human Individuals. PMID:32911083
Finding semantic patterns in omics data using concept rule learning with an ontology-based refinement operator. PMID:32905086
Knowledge-Based Decision Support in Healthcare via Near Field Communication. PMID:32878204
Sex differences in circulating proteins in heart failure with preserved ejection fraction. PMID:32831121
Biomedical Holistic Ontology for People with Rare Diseases. PMID:32825147
OncoPDSS: an evidence-based clinical decision support system for oncology pharmacotherapy at the individual level. PMID:32770988
Signatures of co-deregulated genes and their transcriptional regulators in colorectal cancer. PMID:32737302
Network-based characterization of disease-disease relationships in terms of drugs and therapeutic targets. PMID:32657408
UFO: A tool for unifying biomedical ontology-based semantic similarity calculation, enrichment analysis and visualization. PMID:32645039
Extracellular proteostasis prevents aggregation during pathogenic attack. PMID:32641833
Ontology-driven aspect-based sentiment analysis classification: An infodemiological case study regarding infectious diseases in Latin America. PMID:32572291
CIDO, a community-based ontology for coronavirus disease knowledge and data integration, sharing, and analysis. PMID:32533075
Human gene and disease associations for clinical-genomics and precision medicine research. PMID:32508008
Aggregation and analysis of indication-symptom relationships for drugs approved in the USA. PMID:32495081
GlyGen data model and processing workflow. PMID:32324859
Bootstrapping Adversarial Learning of Biomedical Ontology Alignments. PMID:32308857
DES-ROD: Exploring Literature to Develop New Links between RNA Oxidation and Human Diseases. PMID:32308806
A structured model for immune exposures. PMID:32283555
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
MEDICASCY: A Machine Learning Approach for Predicting Small-Molecule Drug Side Effects, Indications, Efficacy, and Modes of Action. PMID:32237745
A random forest based computational model for predicting novel lncRNA-disease associations. PMID:32216744
Temporal changes in the gene expression heterogeneity during brain development and aging. PMID:32139741
ncRPheno: a comprehensive database platform for identification and validation of disease related noncoding RNAs. PMID:32122231
Annotating and detecting phenotypic information for chronic obstructive pulmonary disease. PMID:31984360
Patient similarity by joint matrix trifactorization to identify subgroups in acute myeloid leukemia. PMID:31984320
Ontology-driven integrative analysis of omics data through Onassis. PMID:31959844
Mechanisms of tissue and cell-type specificity in heritable traits and diseases. PMID:31913361
GBDTCDA: Predicting circRNA-disease Associations Based on Gradient Boosting Decision Tree with Multiple Biological Data Fusion. PMID:31853227
MeinteR: A framework to prioritize DNA methylation aberrations based on conformational and cis-regulatory element enrichment. PMID:31844073
dictyBase and the Dicty Stock Center (version 2.0) - a progress report. PMID:31840793
LncDisAP: a computation model for LncRNA-disease association prediction based on multiple biological datasets. PMID:31787106
Standard operating procedure for curation and clinical interpretation of variants in cancer. PMID:31779674
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
Prioritizing candidate diseases-related metabolites based on literature and functional similarity. PMID:31760947
Identifying Cancer genes by combining two-rounds RWR based on multiple biological data. PMID:31760937
Prediction of disease-related metabolites using bi-random walks. PMID:31730648
HisgAtlas 1.0: a human immunosuppression gene database. PMID:31725860
LncTarD: a manually-curated database of experimentally-supported functional lncRNA-target regulations in human diseases. PMID:31713618
The reactome pathway knowledgebase. PMID:31691815
Cisplatin-resistant triple-negative breast cancer subtypes: multiple mechanisms of resistance. PMID:31684899
MIENTURNET: an interactive web tool for microRNA-target enrichment and network-based analysis. PMID:31684860
ENdb: a manually curated database of experimentally supported enhancers for human and mouse. PMID:31665430
Pan-cancer whole-genome analyses of metastatic solid tumours. PMID:31645765
Predicting circRNA-Disease Associations Based on Improved Collaboration Filtering Recommendation System With Multiple Data. PMID:31608124
Debutant iOS app and gene-disease complexities in clinical genomics and precision medicine. PMID:31586224
gutMDisorder: a comprehensive database for dysbiosis of the gut microbiota in disorders and interventions. PMID:31584099
Predicting circRNA-Disease Associations Based on circRNA Expression Similarity and Functional Similarity. PMID:31572444
Ontology based mining of pathogen-disease associations from literature. PMID:31533864
Predicting drug-induced transcriptome responses of a wide range of human cell lines by a novel tensor-train decomposition algorithm. PMID:31510663
A Survey of Gene Prioritization Tools for Mendelian and Complex Human Diseases. PMID:31494632
Using Twitter to Understand the Human Bowel Disease Community: Exploratory Analysis of Key Topics. PMID:31411142
Determination of chemical-disease risk values to prioritize connections between environmental factors, genetic variants, and human diseases. PMID:31323264
Integrating biomedical research and electronic health records to create knowledge-based biologically meaningful machine-readable embeddings. PMID:31292438
Exploring the dark genome: implications for precision medicine. PMID:31270560
A genetics-led approach defines the drug target landscape of 30 immune-related traits. PMID:31253980
Literature-Based Enrichment Insights into Redox Control of Vascular Biology. PMID:31223421
CoCoScore: context-aware co-occurrence scoring for text mining applications using distant supervision. PMID:31199464
ResMarkerDB: a database of biomarkers of response to antibody therapy in breast and colorectal cancer. PMID:31169290
An Effective Method to Measure Disease Similarity Using Gene and Phenotype Associations. PMID:31164903
PathoPhenoDB, linking human pathogens to their phenotypes in support of infectious disease research. PMID:31160594
ALS blood expression profiling identifies new biomarkers, patient subgroups, and evidence for neutrophilia and hypoxia. PMID:31118040
Tissue-specific genes as an underutilized resource in drug discovery. PMID:31076736
Pathway-specific protein domains are predictive for human diseases. PMID:31075101
ODAE: Ontology-based systematic representation and analysis of drug adverse events and its usage in study of adverse events given different patient age and disease conditions. PMID:31074377
Plasma protein biomarkers and their association with mutually exclusive cardiovascular phenotypes: the FIBRO-TARGETS case-control analyses. PMID:31062082
HumCFS: a database of fragile sites in human chromosomes. PMID:30999860
exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids. PMID:30951672
Quantitative evaluation of ontology design patterns for combining pathology and anatomy ontologies. PMID:30858527
Design, implementation, and operation of a rapid, robust named entity recognition web service. PMID:30850898
Convergent perturbation of the human domain-resolved interactome by viruses and mutations inducing similar disease phenotypes. PMID:30759076
Utility of the JAX Clinical Knowledgebase in capture and assessment of complex genomic cancer data. PMID:30675517
Use case driven evaluation of open databases for pediatric cancer research. PMID:30675185
The utility of phenomics in diagnosis of inherited metabolic disorders. PMID:30651242
Restructured GEO: restructuring Gene Expression Omnibus metadata for genome dynamics analysis. PMID:30649296
Integrating ontologies of human diseases, phenotypes, and radiological diagnosis. PMID:30624645
Prediction of deleterious mutations in coding regions of mammals with transfer learning. PMID:30622632
BO-LSTM: classifying relations via long short-term memory networks along biomedical ontologies. PMID:30616557
Large-scale mining disease comorbidity relationships from post-market drug adverse events surveillance data. PMID:30591027
iTextMine: integrated text-mining system for large-scale knowledge extraction from the literature. PMID:30576489
Early-onset inflammatory bowel disease as a model disease to identify key regulators of immune homeostasis mechanisms. PMID:30565237
Integrating molecular networks with genetic variant interpretation for precision medicine. PMID:30548534
GM604 regulates developmental neurogenesis pathways and the expression of genes associated with amyotrophic lateral sclerosis. PMID:30524706
MER: a shell script and annotation server for minimal named entity recognition and linking. PMID:30519990
Non-coding Class Switch Recombination-Related Transcription in Human Normal and Pathological Immune Responses. PMID:30519242
Improving the Gene Ontology Resource to Facilitate More Informative Analysis and Interpretation of Alzheimer's Disease Data. PMID:30501127
A Review of Current Standards and the Evolution of Histopathology Nomenclature for Laboratory Animals. PMID:30476141
A reference set of curated biomedical data and metadata from clinical case reports. PMID:30457569
BioJupies: Automated Generation of Interactive Notebooks for RNA-Seq Data Analysis in the Cloud. PMID:30447998
IID 2018 update: context-specific physical protein-protein interactions in human, model organisms and domesticated species. PMID:30407591
ECO, the Evidence & Conclusion Ontology: community standard for evidence information. PMID:30407590
Human Disease Ontology 2018 update: classification, content and workflow expansion. PMID:30407550
Identification of key differentially expressed MicroRNAs in cancer patients through pan-cancer analysis. PMID:30384176
HMDD v3.0: a database for experimentally supported human microRNA-disease associations. PMID:30364956
Heterogeneous network embedding for identifying symptom candidate genes. PMID:30357378
The jPOST environment: an integrated proteomics data repository and database. PMID:30295851
Knowledge-based biomedical Data Science. PMID:30294517
LncRNADisease 2.0: an updated database of long non-coding RNA-associated diseases. PMID:30285109
Identifying High-Priority Proteins Across the Human Diseasome Using Semantic Similarity. PMID:30256117
Viruses.STRING: A Virus-Host Protein-Protein Interaction Database. PMID:30249048
The Comparative Toxicogenomics Database: update 2019. PMID:30247620
ATD: a comprehensive bioinformatics resource for deciphering the association of autophagy and diseases. PMID:30239683
DES-Mutation: System for Exploring Links of Mutations and Diseases. PMID:30190574
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
An automated identification and analysis of ontological terms in gastrointestinal diseases and nutrition-related literature provides useful insights. PMID:30065857
BioMuta and BioXpress: mutation and expression knowledgebases for cancer biomarker discovery. PMID:30053270
ChemDIS 2: an update of chemical-disease inference system. PMID:30053236
Phenotype-driven gene prioritization for rare diseases using graph convolution on heterogeneous networks. PMID:29980210
ChemDIS-Mixture: an online tool for analyzing potential interaction effects of chemical mixtures. PMID:29968796
Proximal Pathway Enrichment Analysis for Targeting Comorbid Diseases via Network Endopharmacology. PMID:29932108
Exploring the molecular pathogenesis associated with T-cell prolymphocytic leukemia based on a comprehensive bioinformatics analysis. PMID:29928415
Sustainable data and metadata management at the BD2K-LINCS Data Coordination and Integration Center. PMID:29917015
Genome sequencing uncovers phenocopies in primary progressive multiple sclerosis. PMID:29908077
GNOMICS: A one-stop shop for biomedical and genomic data. PMID:29888054
The Problems of Realism-Based Ontology Design: a Case Study in Creating Definitions for an Application Ontology for Diabetes Camps. PMID:29854221
Towards a complete map of the human long non-coding RNA transcriptome. PMID:29795125
CoNVaQ: a web tool for copy number variation-based association studies. PMID:29776329
Using WormBase: A Genome Biology Resource for Caenorhabditis elegans and Related Nematodes. PMID:29761466
Neutral Theory, Disease Mutations, and Personal Exomes. PMID:29688514
BioDataome: a collection of uniformly preprocessed and automatically annotated datasets for data-driven biology. PMID:29688366
FAIR principles and the IEDB: short-term improvements and a long-term vision of OBO-foundry mediated machine-actionable interoperability. PMID:29688354
A Systems Approach to Refine Disease Taxonomy by Integrating Phenotypic and Molecular Networks. PMID:29669699
Disease Ontology: improving and unifying disease annotations across species. PMID:29590633
Heterogeneous network propagation for herb target identification. PMID:29589568
A Genome-Wide Search for Gene-Environment Effects in Isolated Cleft Lip with or without Cleft Palate Triads Points to an Interaction between Maternal Periconceptional Vitamin Use and Variants in ESRRG. PMID:29535761
RNA-Seq Analysis of IL-1B and IL-36 Responses in Epidermal Keratinocytes Identifies a Shared MyD88-Dependent Gene Signature. PMID:29434599
Bio-SimVerb and Bio-SimLex: wide-coverage evaluation sets of word similarity in biomedicine. PMID:29402212
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
The Porphyromonas gingivalis/Host Interactome Shows Enrichment in GWASdb Genes Related to Alzheimer's Disease, Diabetes and Cardiovascular Diseases. PMID:29311898
Measuring disease similarity and predicting disease-related ncRNAs by a novel method. PMID:29297338
Interoperability of Disease Concepts in Clinical and Research Ontologies: Contrasting Coverage and Structure in the Disease Ontology and SNOMED CT. PMID:29295235
Prioritizing chronic obstructive pulmonary disease (COPD) candidate genes in COPD-related networks. PMID:29262568
A framework for exploring associations between biomedical terms in PubMed. PMID:29262548
eGARD: Extracting associations between genomic anomalies and drug responses from text. PMID:29261751
Integrating phenotype ontologies with PhenomeNET. PMID:29258588
Large-scale analysis of disease pathways in the human interactome. PMID:29218874
Linked Registries: Connecting Rare Diseases Patient Registries through a Semantic Web Layer. PMID:29214177
Matching disease and phenotype ontologies in the ontology alignment evaluation initiative. PMID:29197409
The IUPHAR/BPS Guide to PHARMACOLOGY in 2018: updates and expansion to encompass the new guide to IMMUNOPHARMACOLOGY. PMID:29149325
The Reactome Pathway Knowledgebase. PMID:29145629
PedAM: a database for Pediatric Disease Annotation and Medicine. PMID:29126123
Drug target ontology to classify and integrate drug discovery data. PMID:29122012
MNDR v2.0: an updated resource of ncRNA-disease associations in mammals. PMID:29106639
eRAM: encyclopedia of rare disease annotations for precision medicine. PMID:29106618
PDX-MI: Minimal Information for Patient-Derived Tumor Xenograft Models. PMID:29092942
Lnc2Meth: a manually curated database of regulatory relationships between long non-coding RNAs and DNA methylation associated with human disease. PMID:29069510
Global hotspots and correlates of emerging zoonotic diseases. PMID:29066781
Evaluating phenotype-driven approaches for genetic diagnoses from exomes in a clinical setting. PMID:29044180
Systematic integration of biomedical knowledge prioritizes drugs for repurposing. PMID:28936969
Precision annotation of digital samples in NCBI's gene expression omnibus. PMID:28925997
Chronic obstructive pulmonary disease candidate gene prioritization based on metabolic networks and functional information. PMID:28873096
Mouse Genome Informatics (MGI) Resource: Genetic, Genomic, and Biological Knowledgebase for the Laboratory Mouse. PMID:28838066
Extending TCGA queries to automatically identify analogous genomic data from dbGaP. PMID:28794857
An extensible framework and database of infectious disease for biosurveillance. PMID:28784113
The Immune Epitope Database: How Data Are Entered and Retrieved. PMID:28634590
MetaSRA: normalized human sample-specific metadata for the Sequence Read Archive. PMID:28535296
Recent advances in predicting gene-disease associations. PMID:28529714
mTCTScan: a comprehensive platform for annotation and prioritization of mutations affecting drug sensitivity in cancers. PMID:28482068
QueryOR: a comprehensive web platform for genetic variant analysis and prioritization. PMID:28454514
Neuro-symbolic representation learning on biological knowledge graphs. PMID:28449114
GWAB: a web server for the network-based boosting of human genome-wide association data. PMID:28449091
TIN-X: target importance and novelty explorer. PMID:28398460
Profiling transcriptomes of human SH-SY5Y neuroblastoma cells exposed to maleic acid. PMID:28392987
The anatomy of phenotype ontologies: principles, properties and applications. PMID:28387809
Klinefelter syndrome comorbidities linked to increased X chromosome gene dosage and altered protein interactome activity. PMID:28369266
Better living through ontologies at the Immune Epitope Database. PMID:28365732
Predicting disease-related genes using integrated biomedical networks. PMID:28198675
Annotating Mutational Effects on Proteins and Protein Interactions: Designing Novel and Revisiting Existing Protocols. PMID:28188534
Tutorial on Protein Ontology Resources. PMID:28150233
CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer. PMID:28138153
Exploring FlyBase Data Using QuickSearch. PMID:27930807
AAgAtlas 1.0: a human autoantigen database. PMID:27924021
DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants. PMID:27924018
Function-driven discovery of disease genes in zebrafish using an integrated genomics big data resource. PMID:27903883
KBG syndrome involving a single-nucleotide duplication in ANKRD11. PMID:27900361
Open Targets: a platform for therapeutic target identification and validation. PMID:27899665
MalaCards: an amalgamated human disease compendium with diverse clinical and genetic annotation and structured search. PMID:27899610
Efficient Results in Semantic Interoperability for Health Care. Findings from the Section on Knowledge Representation and Management. PMID:27830249
Knowledge Representation and Management: a Linked Data Perspective. PMID:27830248
FlyBase at 25: looking to the future. PMID:27799470
DrugCentral: online drug compendium. PMID:27789690
Using FlyBase, a Database of Drosophila Genes and Genomes. PMID:27730573
COEXPEDIA: exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH). PMID:27679477
Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd. PMID:27667448
The Comparative Toxicogenomics Database: update 2017. PMID:27651457
Annotating the Function of the Human Genome with Gene Ontology and Disease Ontology. PMID:27635398
Fusing literature and full network data improves disease similarity computation. PMID:27578323
BioWes-from design of experiment, through protocol to repository, control, standardization and back-tracking. PMID:27454467
Are Randomized Controlled Trials the (G)old Standard? From Clinical Intelligence to Prescriptive Analytics. PMID:27383622
IntNetLncSim: an integrative network analysis method to infer human lncRNA functional similarity. PMID:27323856
Jumping across biomedical contexts using compressive data fusion. PMID:27307649
DermO; an ontology for the description of dermatologic disease. PMID:27296450
Weighted mutual information analysis substantially improves domain-based functional network models. PMID:27207946
MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions. PMID:27076900
A Novel Prioritization Method in Identifying Recurrent Venous Thromboembolism-Related Genes. PMID:27050193
Linking rare and common disease: mapping clinical disease-phenotypes to ontologies in therapeutic target validation. PMID:27011785
LORD: a phenotype-genotype semantically integrated biomedical data tool to support rare disease diagnosis coding in health information systems. PMID:26958175
FlyBase portals to human disease research using Drosophila models. PMID:26935103
EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation. PMID:26896844
Inference of domain-disease associations from domain-protein, protein-disease and disease-disease relationships. PMID:26818594
Epigenome overlap measure (EPOM) for comparing tissue/cell types based on chromatin states. PMID:26817822
The Reactome pathway Knowledgebase. PMID:26656494
GWASdb v2: an update database for human genetic variants identified by genome-wide association studies. PMID:26615194
Lynx: a knowledge base and an analytical workbench for integrative medicine. PMID:26590263
WormBase 2016: expanding to enable helminth genomic research. PMID:26578572
Human genotype-phenotype databases: aims, challenges and opportunities. PMID:26553330
The IUPHAR/BPS Guide to PHARMACOLOGY in 2016: towards curated quantitative interactions between 1300 protein targets and 6000 ligands. PMID:26464438
miRTex: A Text Mining System for miRNA-Gene Relation Extraction. PMID:26407127
OVA: integrating molecular and physical phenotype data from multiple biomedical domain ontologies with variant filtering for enhanced variant prioritization. PMID:26272982
Phenotype-driven strategies for exome prioritization of human Mendelian disease genes. PMID:26229552
The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease. PMID:26119816
ZFIN, The zebrafish model organism database: Updates and new directions. PMID:26097180
The Disease Ontology: fostering interoperability between biological and clinical human disease-related data. PMID:26093607
ChemDIS: a chemical-disease inference system based on chemical-protein interactions. PMID:26078786
Analysis of the human diseasome using phenotype similarity between common, genetic, and infectious diseases. PMID:26051359
IMP 2.0: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks. PMID:25969450
Generating a focused view of disease ontology cancer terms for pan-cancer data integration and analysis. PMID:25841438
From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations PubMed citations: 65.

65 articles citing: From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations

Virofree, an Herbal Medicine-Based Formula, Interrupts the Viral Infection of Delta and Omicron Variants of SARS-CoV-2. PMID:35860023
Risk Prediction of Cardiovascular Events by Exploration of Molecular Data with Explainable Artificial Intelligence. PMID:34638627
UFO: A tool for unifying biomedical ontology-based semantic similarity calculation, enrichment analysis and visualization. PMID:32645039
Data-driven method to enhance craniofacial and oral phenotype vocabularies. PMID:31668172
GWAS Central: a comprehensive resource for the discovery and comparison of genotype and phenotype data from genome-wide association studies. PMID:31612961
Analysis of the role of DAMTC in lung adenocarcinoma cells based on the DNA microarrays. PMID:31186684
Thyroid hormone influences brain gene expression programs and behaviors in later generations by altering germ line epigenetic information. PMID:30356120
ChemDIS 2: an update of chemical-disease inference system. PMID:30053236
ChemDIS-Mixture: an online tool for analyzing potential interaction effects of chemical mixtures. PMID:29968796
Integrative gene ontology and network analysis of coronary artery disease associated genes suggests potential role of ErbB pathway gene EGFR. PMID:29328373
Prenatal Exposure to a Maternal High-Fat Diet Affects Histone Modification of Cardiometabolic Genes in Newborn Rats. PMID:28425976
Profiling transcriptomes of human SH-SY5Y neuroblastoma cells exposed to maleic acid. PMID:28392987
Targeted Proteomics for Multiplexed Verification of Markers of Colorectal Tumorigenesis. PMID:28062797
BLAT2DOLite: An Online System for Identifying Significant Relationships between Genetic Sequences and Diseases. PMID:27315278
SOX7 co-regulates Wnt/β-catenin signaling with Axin-2: both expressed at low levels in breast cancer. PMID:27188720
GCGene: a gene resource for gastric cancer with literature evidence. PMID:27127885
Topology based identification and comprehensive classification of four-transmembrane helix containing proteins (4TMs) in the human genome. PMID:27030248
REGene: a literature-based knowledgebase of animal regeneration that bridge tissue regeneration and cancer. PMID:26975833
CSGene: a literature-based database for cell senescence genes and its application to identify critical cell aging pathways and associated diseases. PMID:26775705
Altered expression of mRNA profiles in blood of early-onset schizophrenia. PMID:26733343
ECGene: A Literature-Based Knowledgebase of Endometrial Cancer Genes. PMID:26699919
GWASdb v2: an update database for human genetic variants identified by genome-wide association studies. PMID:26615194
An evidence-based knowledgebase of metastasis suppressors to identify key pathways relevant to cancer metastasis. PMID:26486520
Identification of cancer-related genes and motifs in the human gene regulatory network. PMID:26243828
Development of an Ontology for Periodontitis. PMID:26140188
dbEMT: an epithelial-mesenchymal transition associated gene resource. PMID:26099468
ChemDIS: a chemical-disease inference system based on chemical-protein interactions. PMID:26078786
Pedican: an online gene resource for pediatric cancers with literature evidence. PMID:26073932
Exploring the structure and function of temporal networks with dynamic graphlets. PMID:26072480
Inferring drug-disease associations based on known protein complexes. PMID:26044949
Network-based prediction and knowledge mining of disease genes. PMID:26043920
Network-based association of hypoxia-responsive genes with cardiovascular diseases. PMID:25530704
Assessment of subnetwork detection methods for breast cancer. PMID:25520555
Short-term airborne particulate matter exposure alters the epigenetic landscape of human genes associated with the mitogen-activated protein kinase network: a cross-sectional study. PMID:25395096
Finding pathway-modulating genes from a novel Ontology Fingerprint-derived gene network. PMID:25063300
comoR: a software for disease comorbidity risk assessment. PMID:25045465
Network analysis of inflammatory genes and their transcriptional regulators in coronary artery disease. PMID:24736319
Metadata Standard and Data Exchange Specifications to Describe, Model, and Integrate Complex and Diverse High-Throughput Screening Data from the Library of Integrated Network-based Cellular Signatures (LINCS). PMID:24518066
An evidence-based knowledgebase of pulmonary arterial hypertension to identify genes and pathways relevant to pathogenesis. PMID:24448676
Evaluation and cross-comparison of lexical entities of biological interest (LexEBI). PMID:24124474
The ontology of craniofacial development and malformation for translational craniofacial research. PMID:24124010
Selective anticancer agents suppress aging in Drosophila. PMID:24096697
IQdb: an intelligence quotient score-associated gene resource for human intelligence. PMID:24030781
A genome- and phenome-wide association study to identify genetic variants influencing platelet count and volume and their pleiotropic effects. PMID:24026423
Network topology reveals key cardiovascular disease genes. PMID:23977067
Transcriptional events during the recovery from MRSA lung infection: a mouse pneumonia model. PMID:23936388
Linezolid Exerts Greater Bacterial Clearance but No Modification of Host Lung Gene Expression Profiling: A Mouse MRSA Pneumonia Model. PMID:23826353
InterMOD: integrated data and tools for the unification of model organism research. PMID:23652793
The computational analysis of human testis transcriptome reveals closer ties to pluripotency. PMID:23531778
Formalization, annotation and analysis of diverse drug and probe screening assay datasets using the BioAssay Ontology (BAO). PMID:23155465
TSGene: a web resource for tumor suppressor genes. PMID:23066107
Microarray analysis revealing common and distinct functions of promyelocytic leukemia protein (PML) and tumor necrosis factor alpha (TNFα) signaling in endothelial cells. PMID:22947142
Context-specific protein network miner--an online system for exploring context-specific protein interaction networks from the literature. PMID:22493694
Functional repertoire, molecular pathways and diseases associated with 3D domain swapping in the human proteome. PMID:22472218
Identifying highly conserved and highly differentiated gene ontology categories in human populations. PMID:22140477
GWASdb: a database for human genetic variants identified by genome-wide association studies. PMID:22139925
AutismKB: an evidence-based knowledgebase of autism genetics. PMID:22139918
Disease Ontology: a backbone for disease semantic integration. PMID:22080554
Disease gene interaction pathways: a potential framework for how disease genes associate by disease-risk modules. PMID:21915342
KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. PMID:21715386
DOSim: an R package for similarity between diseases based on Disease Ontology. PMID:21714896
Transactional database transformation and its application in prioritizing human disease genes. PMID:21422495
Identifying informative subsets of the Gene Ontology with information bottleneck methods. PMID:20702400
Phenotype ontologies for mouse and man: bridging the semantic gap. PMID:20427557
A collection of bioconductor methods to visualize gene-list annotations. PMID:20180973
http://dx.doi.org/10.1093/nar/gku1011

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More detailed information about this field from each metasource.

classification
metasource: Fairsharing.org
version: FAIRsharing.org: DOID; Disease Ontology; DOI: https://doi.org/10.25504/FAIRsharing.8b6wfq; Last edited: Aug. 5, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:10 p.m.

disease
metasource: Fairsharing.org
version: FAIRsharing.org: DOID; Disease Ontology; DOI: https://doi.org/10.25504/FAIRsharing.8b6wfq; Last edited: Aug. 5, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:10 p.m.

disease phenotype
metasource: Fairsharing.org
version: FAIRsharing.org: DOID; Disease Ontology; DOI: https://doi.org/10.25504/FAIRsharing.8b6wfq; Last edited: Aug. 5, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:10 p.m.

disease process modeling
metasource: Fairsharing.org
version: FAIRsharing.org: DOID; Disease Ontology; DOI: https://doi.org/10.25504/FAIRsharing.8b6wfq; Last edited: Aug. 5, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:10 p.m.

genetic disorder
metasource: Fairsharing.org
version: FAIRsharing.org: DOID; Disease Ontology; DOI: https://doi.org/10.25504/FAIRsharing.8b6wfq; Last edited: Aug. 5, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:10 p.m.

infection
metasource: Fairsharing.org
version: FAIRsharing.org: DOID; Disease Ontology; DOI: https://doi.org/10.25504/FAIRsharing.8b6wfq; Last edited: Aug. 5, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:10 p.m.

mental health
metasource: Fairsharing.org
version: FAIRsharing.org: DOID; Disease Ontology; DOI: https://doi.org/10.25504/FAIRsharing.8b6wfq; Last edited: Aug. 5, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:10 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

pathology
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:44.576292

ontology and terminology
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:44.576292

medical informatics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:44.576292

molecular interactions, pathways and networks
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:44.576292

rare diseases
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:44.576292

classification disease disease phenotype disease process modeling genetic disorder infection mental health genomics genome annotation terms, ontologies and nomenclature pathology ontology and terminology medical informatics molecular interactions, pathways and networks rare diseases

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