PhenomeBLAST ontology
Names
More detailed information about this field from each metasource.
PhenomeBLAST ontology
metasource: Fairsharing.org
version: FAIRsharing.org: phenomeblast-owl; PhenomeBLAST ontology; DOI: https://doi.org/10.25504/FAIRsharing.evzkcj; Last edited: April 27, 2021, 8:04 a.m.; Last accessed: Jan 03 2022 7:12 p.m.
phenomeblast-owl
metasource: Fairsharing.org
version: FAIRsharing.org: phenomeblast-owl; PhenomeBLAST ontology; DOI: https://doi.org/10.25504/FAIRsharing.evzkcj; Last edited: April 27, 2021, 8:04 a.m.; Last accessed: Jan 03 2022 7:12 p.m.
Names
More detailed information about this field from each metasource.
PhenomeBLAST ontology
metasource: Fairsharing.orgversion: FAIRsharing.org: phenomeblast-owl; PhenomeBLAST ontology; DOI: https://doi.org/10.25504/FAIRsharing.evzkcj; Last edited: April 27, 2021, 8:04 a.m.; Last accessed: Jan 03 2022 7:12 p.m.
phenomeblast-owl
metasource: Fairsharing.orgversion: FAIRsharing.org: phenomeblast-owl; PhenomeBLAST ontology; DOI: https://doi.org/10.25504/FAIRsharing.evzkcj; Last edited: April 27, 2021, 8:04 a.m.; Last accessed: Jan 03 2022 7:12 p.m.
Names
More detailed information about this field from each metasource.
PhenomeBLAST ontology
metasource: Fairsharing.orgversion: FAIRsharing.org: phenomeblast-owl; PhenomeBLAST ontology; DOI: https://doi.org/10.25504/FAIRsharing.evzkcj; Last edited: April 27, 2021, 8:04 a.m.; Last accessed: Jan 03 2022 7:12 p.m.
phenomeblast-owl
metasource: Fairsharing.orgversion: FAIRsharing.org: phenomeblast-owl; PhenomeBLAST ontology; DOI: https://doi.org/10.25504/FAIRsharing.evzkcj; Last edited: April 27, 2021, 8:04 a.m.; Last accessed: Jan 03 2022 7:12 p.m.
PhenomeBLAST is an ontology-based tool that provides a practical implementation of cross-species alignments of phenotypes using ontologies. Both a command-line tool and a web-server are available.
Description
More detailed information about this field from each metasource.
PhenomeBLAST is an ontology-based tool that provides a practical implementation of cross-species alignments of phenotypes using ontologies. Both a command-line tool and a web-server are available.
metasource: Fairsharing.orgversion: FAIRsharing.org: phenomeblast-owl; PhenomeBLAST ontology; DOI: https://doi.org/10.25504/FAIRsharing.evzkcj; Last edited: April 27, 2021, 8:04 a.m.; Last accessed: Jan 03 2022 7:12 p.m.
Webpage:
https://code.google.com/archive/p/phenomeblast/Webpage
More detailed information about this field from each metasource.
https://code.google.com/archive/p/phenomeblast/
metasource: Fairsharing.orgversion: FAIRsharing.org: phenomeblast-owl; PhenomeBLAST ontology; DOI: https://doi.org/10.25504/FAIRsharing.evzkcj; Last edited: April 27, 2021, 8:04 a.m.; Last accessed: Jan 03 2022 7:12 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
PhenomeNET: a whole-phenome approach to disease gene discovery
PMID: 21737429
metasource: Fairsharing.org
version: FAIRsharing.org: phenomeblast-owl; PhenomeBLAST ontology; DOI: https://doi.org/10.25504/FAIRsharing.evzkcj; Last edited: April 27, 2021, 8:04 a.m.; Last accessed: Jan 03 2022 7:12 p.m.
Computational tools for comparative phenomics: the role and promise of ontologies
PMID: 22814867
metasource: Fairsharing.org
version: FAIRsharing.org: phenomeblast-owl; PhenomeBLAST ontology; DOI: https://doi.org/10.25504/FAIRsharing.evzkcj; Last edited: April 27, 2021, 8:04 a.m.; Last accessed: Jan 03 2022 7:12 p.m.
Publications
More detailed information about this field from each metasource.
PhenomeNET: a whole-phenome approach to disease gene discovery
PMID: 21737429
metasource: Fairsharing.org
version: FAIRsharing.org: phenomeblast-owl; PhenomeBLAST ontology; DOI: https://doi.org/10.25504/FAIRsharing.evzkcj; Last edited: April 27, 2021, 8:04 a.m.; Last accessed: Jan 03 2022 7:12 p.m.
Computational tools for comparative phenomics: the role and promise of ontologies
PMID: 22814867
metasource: Fairsharing.org
version: FAIRsharing.org: phenomeblast-owl; PhenomeBLAST ontology; DOI: https://doi.org/10.25504/FAIRsharing.evzkcj; Last edited: April 27, 2021, 8:04 a.m.; Last accessed: Jan 03 2022 7:12 p.m.
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PhenomeNET: a whole-phenome approach to disease gene discovery
PubMed citations: 120.
120 articles citing: PhenomeNET: a whole-phenome approach to disease gene discovery
Evaluating semantic similarity methods for comparison of text-derived phenotype profiles. PMID:35123470
Linking common human diseases to their phenotypes; development of a resource for human phenomics. PMID:34425897
DTI-Voodoo: machine learning over interaction networks and ontology-based background knowledge predicts drug-target interactions. PMID:34320178
Improved characterisation of clinical text through ontology-based vocabulary expansion. PMID:33845909
DeepViral: prediction of novel virus-host interactions from protein sequences and infectious disease phenotypes. PMID:33682875
Establishment and application of information resource of mutant mice in RIKEN BioResource Research Center. PMID:33455583
A review of computational drug repositioning: strategies, approaches, opportunities, challenges, and directions. PMID:33431024
Ontological representation, classification and data-driven computing of phenotypes. PMID:33349245
Transforming the study of organisms: Phenomic data models and knowledge bases. PMID:33232313
DeepPheno: Predicting single gene loss-of-function phenotypes using an ontology-aware hierarchical classifier. PMID:33206638
A Collection of Benchmark Data Sets for Knowledge Graph-based Similarity in the Biomedical Domain. PMID:33181823
Network analysis of autistic disease comorbidities in Chinese children based on ICD-10 codes. PMID:33069223
Predicting candidate genes from phenotypes, functions and anatomical site of expression. PMID:33051643
Semantic similarity and machine learning with ontologies. PMID:33049044
Integration of anatomy ontology data with protein-protein interaction networks improves the candidate gene prediction accuracy for anatomical entities. PMID:33028186
UFO: A tool for unifying biomedical ontology-based semantic similarity calculation, enrichment analysis and visualization. PMID:32645039
BioHackathon 2015: Semantics of data for life sciences and reproducible research. PMID:32308977
Semantic characterization of adverse outcome pathways. PMID:32278258
TarGo: network based target gene selection system for human disease related mouse models. PMID:32257911
Genetic Modifiers and Rare Mendelian Disease. PMID:32106447
Automated Methods Enable Direct Computation on Phenotypic Descriptions for Novel Candidate Gene Prediction. PMID:31998331
Evolving knowledge graph similarity for supervised learning in complex biomedical domains. PMID:31900127
Formal axioms in biomedical ontologies improve analysis and interpretation of associated data. PMID:31821406
HPO2Vec+: Leveraging heterogeneous knowledge resources to enrich node embeddings for the Human Phenotype Ontology. PMID:31255713
PathoPhenoDB, linking human pathogens to their phenotypes in support of infectious disease research. PMID:31160594
Trait ontology analysis based on association mapping studies bridges the gap between crop genomics and Phenomics. PMID:31159731
Predicting disease-related phenotypes using an integrated phenotype similarity measurement based on HPO. PMID:30953559
Quantitative evaluation of ontology design patterns for combining pathology and anatomy ontologies. PMID:30858527
Ontology based text mining of gene-phenotype associations: application to candidate gene prediction. PMID:30809638
Ontology-based semantic mapping of chemical toxicities. PMID:30468866
Semantic Disease Gene Embeddings (SmuDGE): phenotype-based disease gene prioritization without phenotypes. PMID:30423077
Ontology-based validation and identification of regulatory phenotypes. PMID:30423068
An online tool for measuring and visualizing phenotype similarities using HPO. PMID:30367579
OligoPVP: Phenotype-driven analysis of individual genomic information to prioritize oligogenic disease variants. PMID:30279426
Leveraging Collaborative Filtering to Accelerate Rare Disease Diagnosis. PMID:29854225
Inferring ontology graph structures using OWL reasoning. PMID:29304741
Integrating phenotype ontologies with PhenomeNET. PMID:29258588
Matching disease and phenotype ontologies in the ontology alignment evaluation initiative. PMID:29197409
Interrogating Patient-level Genomics and Mouse Phenomics towards Understanding Cytokines in Colorectal Cancer Metastasis. PMID:28815134
Semantic prioritization of novel causative genomic variants. PMID:28414800
The anatomy of phenotype ontologies: principles, properties and applications. PMID:28387809
Evaluating the effect of annotation size on measures of semantic similarity. PMID:28193260
The Human Phenotype Ontology in 2017. PMID:27899602
The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants. PMID:27842607
Drug repurposing for glioblastoma based on molecular subtypes. PMID:27697594
Phenome-based gene discovery provides information about Parkinson's disease drug targets. PMID:27586503
Towards precision medicine-based therapies for glioblastoma: interrogating human disease genomics and mouse phenotypes. PMID:27557118
A Comprehensive Evaluation of Disease Phenotype Networks for Gene Prioritization. PMID:27415759
An integer programming framework for inferring disease complexes from network data. PMID:27307626
DermO; an ontology for the description of dermatologic disease. PMID:27296450
Combining Human Disease Genetics and Mouse Model Phenotypes towards Drug Repositioning for Parkinson's disease. PMID:26958284
Phenoscape: Identifying Candidate Genes for Evolutionary Phenotypes. PMID:26500251
The digital revolution in phenotyping. PMID:26420780
Applications of comparative evolution to human disease genetics. PMID:26338499
Best behaviour? Ontologies and the formal description of animal behaviour. PMID:26215546
Analysis of mammalian gene function through broad-based phenotypic screens across a consortium of mouse clinics. PMID:26214591
Using text mining techniques to extract phenotypic information from the PhenoCHF corpus. PMID:26099853
ZFIN, The zebrafish model organism database: Updates and new directions. PMID:26097180
Disease insights through cross-species phenotype comparisons. PMID:26092691
Phenome-driven disease genetics prediction toward drug discovery. PMID:26072493
Analysis of the human diseasome using phenotype similarity between common, genetic, and infectious diseases. PMID:26051359
Capturing domain knowledge from multiple sources: the rare bone disorders use case. PMID:25926964
Diverse array-designed modes of combination therapies in Fangjiomics. PMID:25864646
The role of ontologies in biological and biomedical research: a functional perspective. PMID:25863278
An ontology approach to comparative phenomics in plants. PMID:25774204
Similarity-based search of model organism, disease and drug effect phenotypes. PMID:25763178
HPOSim: an R package for phenotypic similarity measure and enrichment analysis based on the human phenotype ontology. PMID:25664462
Dsp rul: a spontaneous mouse mutation in desmoplakin as a model of Carvajal-Huerta syndrome. PMID:25659760
PhenomeExpress: a refined network analysis of expression datasets by inclusion of known disease phenotypes. PMID:25631385
Aber-OWL: a framework for ontology-based data access in biology. PMID:25627673
Finding our way through phenotypes. PMID:25562316
PhenUMA: a tool for integrating the biomedical relationships among genes and diseases. PMID:25420641
Organ system heterogeneity DB: a database for the visualization of phenotypes at the organ system level. PMID:25313158
Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome. PMID:25186178
The influence of disease categories on gene candidate predictions from model organism phenotypes. PMID:25093073
Using association rule mining to determine promising secondary phenotyping hypotheses. PMID:24932005
MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network. PMID:24861622
dRiskKB: a large-scale disease-disease risk relationship knowledge base constructed from biomedical text. PMID:24725842
Phenotype ontologies and cross-species analysis for translational research. PMID:24699242
Thematic series on biomedical ontologies in JBMS: challenges and new directions. PMID:24602198
The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery. PMID:24602174
The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. PMID:24217912
Inference of gene-phenotype associations via protein-protein interaction and orthology. PMID:24194887
Mouse model phenotypes provide information about human drug targets. PMID:24158600
Learning to recognize phenotype candidates in the auto-immune literature using SVM re-ranking. PMID:24155869
The Drosophila phenotype ontology. PMID:24138933
Automatically transforming pre- to post-composed phenotypes: EQ-lising HPO and MP. PMID:24131519
Using ontologies to study cell transitions. PMID:24103098
Toward knowledge support for analysis and interpretation of complex traits. PMID:24079802
Manteia, a predictive data mining system for vertebrate genes and its applications to human genetic diseases. PMID:24038354
The mouse pathology ontology, MPATH; structure and applications. PMID:24033988
An integrative, translational approach to understanding rare and orphan genetically based diseases. PMID:23853703
Towards building a disease-phenotype knowledge base: extracting disease-manifestation relationship from literature. PMID:23828786
PhenoDigm: analyzing curated annotations to associate animal models with human diseases. PMID:23660285
Fine mapping for Weaver syndrome in Brown Swiss cattle and the identification of 41 concordant mutations across NRCAM, PNPLA8 and CTTNBP2. PMID:23527149
Decomposing phenotype descriptions for the human skeletal phenome. PMID:23440304
Mining skeletal phenotype descriptions from scientific literature. PMID:23409017
DcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more. PMID:23161684
Text-mining solutions for biomedical research: enabling integrative biology. PMID:23150036
Phenotypic overlap in the contribution of individual genes to CNV pathogenicity revealed by cross-species computational analysis of single-gene mutations in humans, mice and zebrafish. PMID:23104991
Supervised segmentation of phenotype descriptions for the human skeletal phenome using hybrid methods. PMID:23061930
The Units Ontology: a tool for integrating units of measurement in science. PMID:23060432
Ontology-based cross-species integration and analysis of Saccharomyces cerevisiae phenotypes. PMID:23046642
Towards improving phenotype representation in OWL. PMID:23046625
Open biomedical pluralism: formalising knowledge about breast cancer phenotypes. PMID:23046572
Quantitative comparison of mapping methods between Human and Mammalian Phenotype Ontology. PMID:23046555
Evaluation of research in biomedical ontologies. PMID:22962340
The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data. PMID:22961259
The International Mouse Phenotyping Consortium: past and future perspectives on mouse phenotyping. PMID:22940749
Network medicine: linking disorders. PMID:22825316
Computational tools for comparative phenomics: the role and promise of ontologies. PMID:22814867
Co-clustering phenome-genome for phenotype classification and disease gene discovery. PMID:22735708
Improving disease gene prioritization by comparing the semantic similarity of phenotypes in mice with those of human diseases. PMID:22719993
Identifying aberrant pathways through integrated analysis of knowledge in pharmacogenomics. PMID:22711793
Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL. PMID:22541594
Mouse genetic and phenotypic resources for human genetics. PMID:22422677
MouseFinder: Candidate disease genes from mouse phenotype data. PMID:22331800
A comprehensive dataset of genes with a loss-of-function mutant phenotype in Arabidopsis. PMID:22247268
Exploring the elephant: histopathology in high-throughput phenotyping of mutant mice. PMID:22028326
New approaches to the representation and analysis of phenotype knowledge in human diseases and their animal models. PMID:21987712 -
Computational tools for comparative phenomics: the role and promise of ontologies
PubMed citations: 11.
11 articles citing: Computational tools for comparative phenomics: the role and promise of ontologies
Missing Links Between Gene Function and Physiology in Genomics. PMID:35295568
PathoPhenoDB, linking human pathogens to their phenotypes in support of infectious disease research. PMID:31160594
Integrating phenotype ontologies with PhenomeNET. PMID:29258588
Applications of comparative evolution to human disease genetics. PMID:26338499
Disease insights through cross-species phenotype comparisons. PMID:26092691
Diverse array-designed modes of combination therapies in Fangjiomics. PMID:25864646
An ontology approach to comparative phenomics in plants. PMID:25774204
Similarity-based search of model organism, disease and drug effect phenotypes. PMID:25763178
Phage therapy: eco-physiological pharmacology. PMID:25031881
Phenotypic overlap in the contribution of individual genes to CNV pathogenicity revealed by cross-species computational analysis of single-gene mutations in humans, mice and zebrafish. PMID:23104991
The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data. PMID:22961259
Tags:
Tags
More detailed information about this field from each metasource.
molecular interaction
metasource: Fairsharing.org
version: FAIRsharing.org: phenomeblast-owl; PhenomeBLAST ontology; DOI: https://doi.org/10.25504/FAIRsharing.evzkcj; Last edited: April 27, 2021, 8:04 a.m.; Last accessed: Jan 03 2022 7:12 p.m.
phenotype
metasource: Fairsharing.org
version: FAIRsharing.org: phenomeblast-owl; PhenomeBLAST ontology; DOI: https://doi.org/10.25504/FAIRsharing.evzkcj; Last edited: April 27, 2021, 8:04 a.m.; Last accessed: Jan 03 2022 7:12 p.m.
Tags
More detailed information about this field from each metasource.
molecular interaction
metasource: Fairsharing.orgversion: FAIRsharing.org: phenomeblast-owl; PhenomeBLAST ontology; DOI: https://doi.org/10.25504/FAIRsharing.evzkcj; Last edited: April 27, 2021, 8:04 a.m.; Last accessed: Jan 03 2022 7:12 p.m.
phenotype
metasource: Fairsharing.orgversion: FAIRsharing.org: phenomeblast-owl; PhenomeBLAST ontology; DOI: https://doi.org/10.25504/FAIRsharing.evzkcj; Last edited: April 27, 2021, 8:04 a.m.; Last accessed: Jan 03 2022 7:12 p.m.
molecular interaction phenotype
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