Using Phenotype Ontologies in GVF
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Using Phenotype Ontologies in GVF
metasource: Fairsharing.org
version: FAIRsharing.org: GVF Guidelines; Using Phenotype Ontologies in GVF; DOI: https://doi.org/10.25504/FAIRsharing.h1v36j; Last edited: Feb. 13, 2020, 2:56 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
GVF Guidelines
metasource: Fairsharing.org
version: FAIRsharing.org: GVF Guidelines; Using Phenotype Ontologies in GVF; DOI: https://doi.org/10.25504/FAIRsharing.h1v36j; Last edited: Feb. 13, 2020, 2:56 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
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Using Phenotype Ontologies in GVF
metasource: Fairsharing.orgversion: FAIRsharing.org: GVF Guidelines; Using Phenotype Ontologies in GVF; DOI: https://doi.org/10.25504/FAIRsharing.h1v36j; Last edited: Feb. 13, 2020, 2:56 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
GVF Guidelines
metasource: Fairsharing.orgversion: FAIRsharing.org: GVF Guidelines; Using Phenotype Ontologies in GVF; DOI: https://doi.org/10.25504/FAIRsharing.h1v36j; Last edited: Feb. 13, 2020, 2:56 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
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Using Phenotype Ontologies in GVF
metasource: Fairsharing.orgversion: FAIRsharing.org: GVF Guidelines; Using Phenotype Ontologies in GVF; DOI: https://doi.org/10.25504/FAIRsharing.h1v36j; Last edited: Feb. 13, 2020, 2:56 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
GVF Guidelines
metasource: Fairsharing.orgversion: FAIRsharing.org: GVF Guidelines; Using Phenotype Ontologies in GVF; DOI: https://doi.org/10.25504/FAIRsharing.h1v36j; Last edited: Feb. 13, 2020, 2:56 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
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This guideline describes a set of best practices when using phenotype ontologies to annotate genomic variant files using Genome Variation Format (GVF) and the Sequence Ontology.
Description
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This guideline describes a set of best practices when using phenotype ontologies to annotate genomic variant files using Genome Variation Format (GVF) and the Sequence Ontology.
metasource: Fairsharing.orgversion: FAIRsharing.org: GVF Guidelines; Using Phenotype Ontologies in GVF; DOI: https://doi.org/10.25504/FAIRsharing.h1v36j; Last edited: Feb. 13, 2020, 2:56 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
Webpage:
http://www.sequenceontology.org/so_wiki/index.php/Using_Phenotype_Ontologies_in_GVFWebpage
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http://www.sequenceontology.org/so_wiki/index.php/Using_Phenotype_Ontologies_in_GVF
metasource: Fairsharing.orgversion: FAIRsharing.org: GVF Guidelines; Using Phenotype Ontologies in GVF; DOI: https://doi.org/10.25504/FAIRsharing.h1v36j; Last edited: Feb. 13, 2020, 2:56 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
Publications:
Publications
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Integrating phenotype ontologies across multiple species
PMID: 20064205
metasource: Fairsharing.org
version: FAIRsharing.org: GVF Guidelines; Using Phenotype Ontologies in GVF; DOI: https://doi.org/10.25504/FAIRsharing.h1v36j; Last edited: Feb. 13, 2020, 2:56 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
Publications
More detailed information about this field from each metasource.
Integrating phenotype ontologies across multiple species
PMID: 20064205
metasource: Fairsharing.org
version: FAIRsharing.org: GVF Guidelines; Using Phenotype Ontologies in GVF; DOI: https://doi.org/10.25504/FAIRsharing.h1v36j; Last edited: Feb. 13, 2020, 2:56 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
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Integrating phenotype ontologies across multiple species
PubMed citations: 148.
148 articles citing: Integrating phenotype ontologies across multiple species
Screens in fly and beetle reveal vastly divergent gene sets required for developmental processes. PMID:35135533
FAIR data representation in times of eScience: a comparison of instance-based and class-based semantic representations of empirical data using phenotype descriptions as example. PMID:34823588
A starting guide to root ecology: strengthening ecological concepts and standardising root classification, sampling, processing and trait measurements. PMID:34608637
Planarian Anatomy Ontology: a resource to connect data within and across experimental platforms. PMID:34318308
Applying FAIR Principles to Plant Phenotypic Data Management in GnpIS. PMID:33313522
Transforming the study of organisms: Phenomic data models and knowledge bases. PMID:33232313
Predicting candidate genes from phenotypes, functions and anatomical site of expression. PMID:33051643
Semantic similarity and machine learning with ontologies. PMID:33049044
BiPOm: a rule-based ontology to represent and infer molecule knowledge from a biological process-centered viewpoint. PMID:32703160
Semantic characterization of adverse outcome pathways. PMID:32278258
Automated Methods Enable Direct Computation on Phenotypic Descriptions for Novel Candidate Gene Prediction. PMID:31998331
The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species. PMID:31701156
A Logical Model of Homology for Comparative Biology. PMID:31596473
Phenotype annotation with the ontology of microbial phenotypes (OMP). PMID:31307550
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
Review: New sensors and data-driven approaches-A path to next generation phenomics. PMID:31003608
Quantitative evaluation of ontology design patterns for combining pathology and anatomy ontologies. PMID:30858527
Annotation of phenotypes using ontologies: a gold standard for the training and evaluation of natural language processing systems. PMID:30576485
Ontology-based semantic mapping of chemical toxicities. PMID:30468866
Biomedical ontology alignment: an approach based on representation learning. PMID:30111369
Discovering Health Benefits of Phytochemicals with Integrated Analysis of the Molecular Network, Chemical Properties and Ethnopharmacological Evidence. PMID:30096807
Creating a Structured AOP Knowledgebase via Ontology-Based Annotations. PMID:30057931
High-throughput mouse phenomics for characterizing mammalian gene function. PMID:29626206
Where to search top-K biomedical ontologies? PMID:29579141
Tackling the challenges of matching biomedical ontologies. PMID:29335022
Automated Integration of Trees and Traits: A Case Study Using Paired Fin Loss Across Teleost Fishes. PMID:29325126
Improving the interoperability of biomedical ontologies with compound alignments. PMID:29316968
Integrating phenotype ontologies with PhenomeNET. PMID:29258588
Semantic prioritization of novel causative genomic variants. PMID:28414800
The anatomy of phenotype ontologies: principles, properties and applications. PMID:28387809
Drosophila and genome-wide association studies: a review and resource for the functional dissection of human complex traits. PMID:28151408
The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species. PMID:27899636
The Zebrafish Model Organism Database: new support for human disease models, mutation details, gene expression phenotypes and searching. PMID:27899582
The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants. PMID:27842607
Modeling biochemical pathways in the gene ontology. PMID:27589964
A scientist's guide for submitting data to ZFIN. PMID:27443940
The cellular microscopy phenotype ontology. PMID:27195102
Data Sources for Trait Databases: Comparing the Phenomic Content of Monographs and Evolutionary Matrices. PMID:27191170
Capturing phenotypes for precision medicine. PMID:27148566
Reporting phenotypes in mouse models when considering body size as a potential confounder. PMID:26865945
PhenoMiner: from text to a database of phenotypes associated with OMIM diseases. PMID:26507285
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
Use of model organism and disease databases to support matchmaking for human disease gene discovery. PMID:26269093
The iBeetle large-scale RNAi screen reveals gene functions for insect development and physiology. PMID:26215380
Development of an Ontology for Periodontitis. PMID:26140188
The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease. PMID:26119816
Disease insights through cross-species phenotype comparisons. PMID:26092691
Analysis of the human diseasome using phenotype similarity between common, genetic, and infectious diseases. PMID:26051359
Toward Synthesizing Our Knowledge of Morphology: Using Ontologies and Machine Reasoning to Extract Presence/Absence Evolutionary Phenotypes across Studies. PMID:26018570
Moving the mountain: analysis of the effort required to transform comparative anatomy into computable anatomy. PMID:25972520
TermGenie - a web-application for pattern-based ontology class generation. PMID:25937883
Linking gene expression to phenotypes via pathway information. PMID:25901272
The role of ontologies in biological and biomedical research: a functional perspective. PMID:25863278
eNanoMapper: harnessing ontologies to enable data integration for nanomaterial risk assessment. PMID:25815161
Supporting the annotation of chronic obstructive pulmonary disease (COPD) phenotypes with text mining workflows. PMID:25789153
An ontology approach to comparative phenomics in plants. PMID:25774204
Similarity-based search of model organism, disease and drug effect phenotypes. PMID:25763178
A bioinformatics expert system linking functional data to anatomical outcomes in limb regeneration. PMID:25729585
Reasoning over taxonomic change: exploring alignments for the Perelleschus use case. PMID:25700173
Aber-OWL: a framework for ontology-based data access in biology. PMID:25627673
EXACT2: the semantics of biomedical protocols. PMID:25472549
An ontology for microbial phenotypes. PMID:25433798
Annotation of phenotypic diversity: decoupling data curation and ontology curation using Phenex. PMID:25411634
iBeetle-Base: a database for RNAi phenotypes in the red flour beetle Tribolium castaneum. PMID:25378303
Organ system heterogeneity DB: a database for the visualization of phenotypes at the organ system level. PMID:25313158
Molecularly and clinically related drugs and diseases are enriched in phenotypically similar drug-disease pairs. PMID:25276232
Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology. PMID:25140222
The influence of disease categories on gene candidate predictions from model organism phenotypes. PMID:25093073
The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation. PMID:25068035
Standardized description of scientific evidence using the Evidence Ontology (ECO). PMID:25052702
Phenotype ontologies and cross-species analysis for translational research. PMID:24699242
Linking tissues to phenotypes using gene expression profiles. PMID:24634472
Semantic integration of gene expression analysis tools and data sources using software connectors. PMID:24341380
RARGE II: an integrated phenotype database of Arabidopsis mutant traits using a controlled vocabulary. PMID:24272250
Analyzing gene expression data in mice with the Neuro Behavior Ontology. PMID:24177753
Improved exome prioritization of disease genes through cross-species phenotype comparison. PMID:24162188
Mouse model phenotypes provide information about human drug targets. PMID:24158600
Automatically transforming pre- to post-composed phenotypes: EQ-lising HPO and MP. PMID:24131519
The ontology of craniofacial development and malformation for translational craniofacial research. PMID:24124010
Using ontologies to study cell transitions. PMID:24103098
The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments. PMID:24093723
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
TrOn: an anatomical ontology for the beetle Tribolium castaneum. PMID:23936240
An integrative, translational approach to understanding rare and orphan genetically based diseases. PMID:23853703
A knowledge based approach to matching human neurodegenerative disease and animal models. PMID:23717278
Modeling functional Magnetic Resonance Imaging (fMRI) experimental variables in the Ontology of Experimental Variables and Values (OoEVV). PMID:23684873
PhenoDigm: analyzing curated annotations to associate animal models with human diseases. PMID:23660285
FYPO: the fission yeast phenotype ontology. PMID:23658422
A semantic model for species description applied to the ensign wasps (hymenoptera: evaniidae) of New Caledonia. PMID:23652347
Systematic analysis of experimental phenotype data reveals gene functions. PMID:23626672
Decomposing phenotype descriptions for the human skeletal phenome. PMID:23440304
Towards a bioinformatics of patterning: a computational approach to understanding regulative morphogenesis. PMID:23429669
A unified anatomy ontology of the vertebrate skeletal system. PMID:23251424
Semantically enabling a genome-wide association study database. PMID:23244533
H2DB: a heritability database across multiple species by annotating trait-associated genomic loci. PMID:23193255
A revision of Evaniscus (Hymenoptera, Evaniidae) using ontology-based semantic phenotype annotation. PMID:23166458
DcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more. PMID:23161684
Phenotypic overlap in the contribution of individual genes to CNV pathogenicity revealed by cross-species computational analysis of single-gene mutations in humans, mice and zebrafish. PMID:23104991
A UML profile for the OBO relation ontology. PMID:23095840
ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics. PMID:23074187
Cross-Ontology multi-level association rule mining in the Gene Ontology. PMID:23071802
Continuation-like semantics for modeling structural process anomalies. PMID:23046705
Ontology-based cross-species integration and analysis of Saccharomyces cerevisiae phenotypes. PMID:23046642
Towards improving phenotype representation in OWL. PMID:23046625
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
Querying phenotype-genotype relationships on patient datasets using semantic web technology: the example of Cerebrotendinous xanthomatosis. PMID:22849591
Ontologies as integrative tools for plant science. PMID:22847540
Computational tools for comparative phenomics: the role and promise of ontologies. PMID:22814867
Improving disease gene prioritization by comparing the semantic similarity of phenotypes in mice with those of human diseases. PMID:22719993
Three ontologies to define phenotype measurement data. PMID:22654893
Semantic integration of physiology phenotypes with an application to the Cellular Phenotype Ontology. PMID:22539675
NeXML: rich, extensible, and verifiable representation of comparative data and metadata. PMID:22357728
MouseFinder: Candidate disease genes from mouse phenotype data. PMID:22331800
Uberon, an integrative multi-species anatomy ontology. PMID:22293552
Disease Ontology: a backbone for disease semantic integration. PMID:22080554
Improving ontologies by automatic reasoning and evaluation of logical definitions. PMID:22032770
OBML - Ontologies in Biomedicine and Life Sciences. PMID:21996496
New approaches to the representation and analysis of phenotype knowledge in human diseases and their animal models. PMID:21987712
Integrating systems biology models and biomedical ontologies. PMID:21835028
Interoperability between biomedical ontologies through relation expansion, upper-level ontologies and automatic reasoning. PMID:21789201
PhenomeNET: a whole-phenome approach to disease gene discovery. PMID:21737429
Computable visually observed phenotype ontological framework for plants. PMID:21702966
The cognitive paradigm ontology: design and application. PMID:21643732
Developing a kidney and urinary pathway knowledge base. PMID:21624162
PHENOPSIS DB: an information system for Arabidopsis thaliana phenotypic data in an environmental context. PMID:21554668
A common layer of interoperability for biomedical ontologies based on OWL EL. PMID:21343142
Worm Phenotype Ontology: integrating phenotype data within and beyond the C. elegans community. PMID:21261995
Trends in computational biology—2010. PMID:21221103
The RIKEN integrated database of mammals. PMID:21076152
Laboratory mouse models for the human genome-wide associations. PMID:21072174
Interoperability between phenotype and anatomy ontologies. PMID:20971987
ParameciumDB in 2011: new tools and new data for functional and comparative genomics of the model ciliate Paramecium tetraurelia. PMID:20952411
Applying the functional abnormality ontology pattern to anatomical functions. PMID:20618982
The teleost anatomy ontology: anatomical representation for the genomics age. PMID:20547776
Evolutionary characters, phenotypes and ontologies: curating data from the systematic biology literature. PMID:20505755
Phenex: ontological annotation of phenotypic diversity. PMID:20463926
Phenotype ontologies for mouse and man: bridging the semantic gap. PMID:20427557
Cross-product extensions of the Gene Ontology. PMID:20152934
Hematopoietic cell types: prototype for a revised cell ontology. PMID:20123131
Linking human diseases to animal models using ontology-based phenotype annotation. PMID:19956802
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genetic polymorphism
metasource: Fairsharing.org
version: FAIRsharing.org: GVF Guidelines; Using Phenotype Ontologies in GVF; DOI: https://doi.org/10.25504/FAIRsharing.h1v36j; Last edited: Feb. 13, 2020, 2:56 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
phenotype
metasource: Fairsharing.org
version: FAIRsharing.org: GVF Guidelines; Using Phenotype Ontologies in GVF; DOI: https://doi.org/10.25504/FAIRsharing.h1v36j; Last edited: Feb. 13, 2020, 2:56 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
Tags
More detailed information about this field from each metasource.
genetic polymorphism
metasource: Fairsharing.orgversion: FAIRsharing.org: GVF Guidelines; Using Phenotype Ontologies in GVF; DOI: https://doi.org/10.25504/FAIRsharing.h1v36j; Last edited: Feb. 13, 2020, 2:56 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
phenotype
metasource: Fairsharing.orgversion: FAIRsharing.org: GVF Guidelines; Using Phenotype Ontologies in GVF; DOI: https://doi.org/10.25504/FAIRsharing.h1v36j; Last edited: Feb. 13, 2020, 2:56 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
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