Planteome
A resource providing data on bioentities and their associated ontology terms for Plant Biology. The database provides access to ontology-based annotations of genes, phenotypes and germplasms from about 90 plant species. A number of internal and external ontologies are used to annotate the biological data available from this resource.
Description
More detailed information about this field from each metasource.
A resource providing data on bioentities and their associated ontology terms for Plant Biology. The database provides access to ontology-based annotations of genes, phenotypes and germplasms from about 90 plant species. A number of internal and external ontologies are used to annotate the biological data available from this resource.
metasource: Fairsharing.orgversion: FAIRsharing.org: Planteome; Planteome; DOI: https://doi.org/10.25504/FAIRsharing.k0kcjw; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
The Planteome project (http://www.planteome.org) provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project also provides access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. The Planteome project is developing a plant gene annotation platform; Planteome Noctua, to facilitate community engagement. All the Planteome ontologies are publicly available and are maintained at the Planteome GitHub site (https://github.com/Planteome) for sharing, tracking revisions and new requests. The annotated data are freely accessible from the ontology browser (http://browser.planteome.org/amigo) and our data repository.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Webpage:
http://www.planteome.orgWebpage
More detailed information about this field from each metasource.
http://www.planteome.org
metasource: Fairsharing.orgversion: FAIRsharing.org: Planteome; Planteome; DOI: https://doi.org/10.25504/FAIRsharing.k0kcjw; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Licence:
Name: Creative Commons Attribution 4.0 International (CC BY 4.0)Licence name
More detailed information about this field from each metasource.
Creative Commons Attribution 4.0 International (CC BY 4.0)
metasource: Fairsharing.orgversion: FAIRsharing.org: Planteome; Planteome; DOI: https://doi.org/10.25504/FAIRsharing.k0kcjw; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
Licence URL
More detailed information about this field from each metasource.
https://creativecommons.org/licenses/by/4.0/
metasource: Fairsharing.orgversion: FAIRsharing.org: Planteome; Planteome; DOI: https://doi.org/10.25504/FAIRsharing.k0kcjw; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
Publications:
(13)
Publications
More detailed information about this field from each metasource.
Finding our way through phenotypes
PMID: 25562316
metasource: Fairsharing.org
version: FAIRsharing.org: Planteome; Planteome; DOI: https://doi.org/10.25504/FAIRsharing.k0kcjw; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations
PMID: 18194960
metasource: Fairsharing.org
version: FAIRsharing.org: Planteome; Planteome; DOI: https://doi.org/10.25504/FAIRsharing.k0kcjw; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
The plant ontology as a tool for comparative plant anatomy and genomic analyses
PMID: 23220694
metasource: Fairsharing.org
version: FAIRsharing.org: Planteome; Planteome; DOI: https://doi.org/10.25504/FAIRsharing.k0kcjw; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and Growth Stages
PMID: 18629207
metasource: Fairsharing.org
version: FAIRsharing.org: Planteome; Planteome; DOI: https://doi.org/10.25504/FAIRsharing.k0kcjw; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics
PMID: 29186578
metasource: Fairsharing.org
version: FAIRsharing.org: Planteome; Planteome; DOI: https://doi.org/10.25504/FAIRsharing.k0kcjw; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant
PMID: 17142475
metasource: Fairsharing.org
version: FAIRsharing.org: Planteome; Planteome; DOI: https://doi.org/10.25504/FAIRsharing.k0kcjw; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
Ontologies as integrative tools for plant science
PMID: 22847540
metasource: Fairsharing.org
version: FAIRsharing.org: Planteome; Planteome; DOI: https://doi.org/10.25504/FAIRsharing.k0kcjw; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
Whole-plant growth stage ontology for angiosperms and its application in plant biology
PMID: 16905665
metasource: Fairsharing.org
version: FAIRsharing.org: Planteome; Planteome; DOI: https://doi.org/10.25504/FAIRsharing.k0kcjw; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
Biological ontologies in rice databases. An introduction to the activities in Gramene and Oryzabase
PMID: 15659431
metasource: Fairsharing.org
version: FAIRsharing.org: Planteome; Planteome; DOI: https://doi.org/10.25504/FAIRsharing.k0kcjw; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
An ontology approach to comparative phenomics in plants
PMID: 25774204
metasource: Fairsharing.org
version: FAIRsharing.org: Planteome; Planteome; DOI: https://doi.org/10.25504/FAIRsharing.k0kcjw; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
The Plant Ontology: A Tool for Plant Genomics
PMID: 26519402
metasource: Fairsharing.org
version: FAIRsharing.org: Planteome; Planteome; DOI: https://doi.org/10.25504/FAIRsharing.k0kcjw; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
AISO: Annotation of Image Segments with Ontologies
PMID: 25584184
metasource: Fairsharing.org
version: FAIRsharing.org: Planteome; Planteome; DOI: https://doi.org/10.25504/FAIRsharing.k0kcjw; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
http://dx.doi.org/10.1093/nar/gkx1152
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications
More detailed information about this field from each metasource.
Finding our way through phenotypes
PMID: 25562316
metasource: Fairsharing.org
version: FAIRsharing.org: Planteome; Planteome; DOI: https://doi.org/10.25504/FAIRsharing.k0kcjw; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations
PMID: 18194960
metasource: Fairsharing.org
version: FAIRsharing.org: Planteome; Planteome; DOI: https://doi.org/10.25504/FAIRsharing.k0kcjw; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
The plant ontology as a tool for comparative plant anatomy and genomic analyses
PMID: 23220694
metasource: Fairsharing.org
version: FAIRsharing.org: Planteome; Planteome; DOI: https://doi.org/10.25504/FAIRsharing.k0kcjw; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and Growth Stages
PMID: 18629207
metasource: Fairsharing.org
version: FAIRsharing.org: Planteome; Planteome; DOI: https://doi.org/10.25504/FAIRsharing.k0kcjw; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics
PMID: 29186578
metasource: Fairsharing.org
version: FAIRsharing.org: Planteome; Planteome; DOI: https://doi.org/10.25504/FAIRsharing.k0kcjw; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant
PMID: 17142475
metasource: Fairsharing.org
version: FAIRsharing.org: Planteome; Planteome; DOI: https://doi.org/10.25504/FAIRsharing.k0kcjw; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
Ontologies as integrative tools for plant science
PMID: 22847540
metasource: Fairsharing.org
version: FAIRsharing.org: Planteome; Planteome; DOI: https://doi.org/10.25504/FAIRsharing.k0kcjw; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
Whole-plant growth stage ontology for angiosperms and its application in plant biology
PMID: 16905665
metasource: Fairsharing.org
version: FAIRsharing.org: Planteome; Planteome; DOI: https://doi.org/10.25504/FAIRsharing.k0kcjw; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
Biological ontologies in rice databases. An introduction to the activities in Gramene and Oryzabase
PMID: 15659431
metasource: Fairsharing.org
version: FAIRsharing.org: Planteome; Planteome; DOI: https://doi.org/10.25504/FAIRsharing.k0kcjw; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
An ontology approach to comparative phenomics in plants
PMID: 25774204
metasource: Fairsharing.org
version: FAIRsharing.org: Planteome; Planteome; DOI: https://doi.org/10.25504/FAIRsharing.k0kcjw; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
The Plant Ontology: A Tool for Plant Genomics
PMID: 26519402
metasource: Fairsharing.org
version: FAIRsharing.org: Planteome; Planteome; DOI: https://doi.org/10.25504/FAIRsharing.k0kcjw; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
AISO: Annotation of Image Segments with Ontologies
PMID: 25584184
metasource: Fairsharing.org
version: FAIRsharing.org: Planteome; Planteome; DOI: https://doi.org/10.25504/FAIRsharing.k0kcjw; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
http://dx.doi.org/10.1093/nar/gkx1152
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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Finding our way through phenotypes
PubMed citations: 77.
77 articles citing: Finding our way through phenotypes
Past and future uses of text mining in ecology and evolution. PMID:35582795
Association of Pathogenic Variants in Hereditary Cancer Genes With Multiple Diseases. PMID:35446370
The Agricultural Genome to Phenome Initiative (AG2PI): creating a shared vision across crop and livestock research communities. PMID:34980221
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
Pleiotropy data resource as a primer for investigating co-morbidities/multi-morbidities and their role in disease. PMID:34524473
Genome Fractionation and Loss of Heterozygosity in Hybrids and Polyploids: Mechanisms, Consequences for Selection, and Link to Gene Function. PMID:34410426
ACO2 clinicobiological dataset with extensive phenotype ontology annotation. PMID:34354088
Many ways to make darker flies: Intra- and interspecific variation in Drosophila body pigmentation components. PMID:34188876
Mapping OMIM Disease-Related Variations on Protein Domains Reveals an Association Among Variation Type, Pfam Models, and Disease Classes. PMID:34026820
Ontological representation, classification and data-driven computing of phenotypes. PMID:33349245
Transforming the study of organisms: Phenomic data models and knowledge bases. PMID:33232313
Hierarchical analysis of ontogenetic time to describe heterochrony and taxonomy of developmental stages. PMID:33184336
Semantic similarity and machine learning with ontologies. PMID:33049044
Machine-learning strategies for testing patterns of morphological variation in small samples: sexual dimorphism in gray wolf (Canis lupus) crania. PMID:32883273
Open Science principles for accelerating trait-based science across the Tree of Life. PMID:32066887
The odonate phenotypic database, a new open data resource for comparative studies of an old insect order. PMID:31831730
Representing glycophenotypes: semantic unification of glycobiology resources for disease discovery. PMID:31735951
Opportunities and Limitations of Crop Phenotyping in Southern European Countries. PMID:31608085
Comparison of Causative Variant Prioritization Tools Using Next-generation Sequencing Data in Japanese Patients with Mendelian Disorders. PMID:31582890
OPA1: 516 unique variants and 831 patients registered in an updated centralized Variome database. PMID:31500643
OryzaGP: rice gene and protein dataset for named-entity recognition. PMID:31307132
Whole-genome duplication and hemoglobin differentiation traits between allopatric populations of Brazilian Odontophrynus americanus species complex (Amphibia, Anura). PMID:31259358
High-throughput profiling and analysis of plant responses over time to abiotic stress. PMID:31245669
Organizing phenotypic data-a semantic data model for anatomy. PMID:31221226
Trait ontology analysis based on association mapping studies bridges the gap between crop genomics and Phenomics. PMID:31159731
Integrating natural history collections and comparative genomics to study the genetic architecture of convergent evolution. PMID:31154982
The Legacy of Sexual Ancestors in Phenotypic Variability, Gene Expression, and Homoeolog Regulation of Asexual Hybrids and Polyploids. PMID:31077330
Integration of Anatomy Ontologies and Evo-Devo Using Structured Markov Models Suggests a New Framework for Modeling Discrete Phenotypic Traits. PMID:30668800
Annotation of phenotypes using ontologies: a gold standard for the training and evaluation of natural language processing systems. PMID:30576485
Computational aspects underlying genome to phenome analysis in plants. PMID:30500991
Rooting Phylogenies and the Tree of Life While Minimizing Ad Hoc and Auxiliary Assumptions. PMID:30364468
Mapping Molecular Datasets Back to the Brain Regions They are Extracted from: Remembering the Native Countries of Hypothalamic Expatriates and Refugees. PMID:30334222
The Comparative Toxicogenomics Database: update 2019. PMID:30247620
Morphological description, character conceptualization and the reconstruction of ancestral states exemplified by the evolution of arthropod hearts. PMID:30235213
A simple developmental model recapitulates complex insect wing venation patterns. PMID:30224459
Deep Phenotyping on Electronic Health Records Facilitates Genetic Diagnosis by Clinical Exomes. PMID:29961570
Chemical-Induced Phenotypes at CTD Help Inform the Predisease State and Construct Adverse Outcome Pathways. PMID:29846728
Measuring phenotype-phenotype similarity through the interactome. PMID:29671400
webpic: A flexible web application for collecting distance and count measurements from images. PMID:29608592
Text-based phenotypic profiles incorporating biochemical phenotypes of inborn errors of metabolism improve phenomics-based diagnosis. PMID:29340838
Investigations on factors influencing HPO-based semantic similarity calculation. PMID:29297376
Mini-Review: The Contribution of Intermediate Phenotypes to GxE Effects on Disorders of Body Composition in the New OMICS Era. PMID:28926971
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 importance of digitized biocollections as a source of trait data and a new VertNet resource. PMID:28025346
The landscape of microbial phenotypic traits and associated genes. PMID:27915291
PHI-base: a new interface and further additions for the multi-species pathogen-host interactions database. PMID:27915230
The Human Phenotype Ontology in 2017. PMID:27899602
Deep phenotyping unveils hidden traits and genetic relations in subtle mutants. PMID:27876787
The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants. PMID:27842607
Redefining 'stress resistance genes', and why it matters. PMID:27702993
Clinical phenotyping in selected national networks: demonstrating the need for high-throughput, portable, and computational methods. PMID:27506131
The Quest for Understanding Phenotypic Variation via Integrated Approaches in the Field Environment. PMID:27482076
Ontology-based Vaccine and Drug Adverse Event Representation and Theory-guided Systematic Causal Network Analysis toward Integrative Pharmacovigilance Research. PMID:27458549
PRECOG: a tool for automated extraction and visualization of fitness components in microbial growth phenomics. PMID:27334112
Genomics: The language of flowers. PMID:27281204
Controlling for Phylogenetic Relatedness and Evolutionary Rates Improves the Discovery of Associations Between Species' Phenotypic and Genomic Differences. PMID:27222536
Data Sources for Trait Databases: Comparing the Phenomic Content of Monographs and Evolutionary Matrices. PMID:27191170
Multi-omic data integration and analysis using systems genomics approaches: methods and applications in animal production, health and welfare. PMID:27130220
MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions. PMID:27076900
The Implicitome: A Resource for Rationalizing Gene-Disease Associations. PMID:26919047
Unravelling the human genome-phenome relationship using phenome-wide association studies. PMID:26875678
Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals. PMID:26870952
Systematic Phenomics Analysis Deconvolutes Genes Mutated in Intellectual Disability into Biologically Coherent Modules. PMID:26748517
Mechanisms of Origin, Phenotypic Effects and Diagnostic Implications of Complex Chromosome Rearrangements. PMID:26732513
Emerging semantics to link phenotype and environment. PMID:26713234
Phenoscape: Identifying Candidate Genes for Evolutionary Phenotypes. PMID:26500251
Human phenotyping on a population scale. PMID:26226359
Publishing and sharing multi-dimensional image data with OMERO. PMID:26223880
Implications of Big Data for cell biology. PMID:26174066
The Genetic Basis of Mendelian Phenotypes: Discoveries, Challenges, and Opportunities. PMID:26166479
PhenStat: A Tool Kit for Standardized Analysis of High Throughput Phenotypic Data. PMID:26147094
Computational methods and resources for the interpretation of genomic variants in cancer. PMID:26111056
The differential view of genotype-phenotype relationships. PMID:26042146
Moving the mountain: analysis of the effort required to transform comparative anatomy into computable anatomy. PMID:25972520
An ontology approach to comparative phenomics in plants. PMID:25774204
MatrixConverter: Facilitating construction of phenomic character matrices. PMID:25699217 -
The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations
PubMed citations: 59.
59 articles citing: The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations
PCMDB: a curated and comprehensive resource of plant cell markers. PMID:34718712
Vision, challenges and opportunities for a Plant Cell Atlas. PMID:34491200
Opportunities and limits of controlled-environment plant phenotyping for climate response traits. PMID:34302493
WTO, an ontology for wheat traits and phenotypes in scientific publications. PMID:32634868
FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration. PMID:31304272
Modeling Crop Genetic Resources Phenotyping Information Systems. PMID:31281323
Trait ontology analysis based on association mapping studies bridges the gap between crop genomics and Phenomics. PMID:31159731
Semi-automatic Extraction of Plants Morphological Characters from Taxonomic Descriptions Written in Spanish. PMID:29991903
Where to search top-K biomedical ontologies? PMID:29579141
New extension software modules to enhance searching and display of transcriptome data in Tripal databases. PMID:29220446
The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics. PMID:29186578
CottonFGD: an integrated functional genomics database for cotton. PMID:28595571
Identifying novel fruit-related genes in Arabidopsis thaliana based on the random walk with restart algorithm. PMID:28472169
The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants. PMID:27842607
A Shortest-Path-Based Method for the Analysis and Prediction of Fruit-Related Genes in Arabidopsis thaliana. PMID:27434024
The BioHub Knowledge Base: Ontology and Repository for Sustainable Biosourcing. PMID:27246819
expVIP: a Customizable RNA-seq Data Analysis and Visualization Platform. PMID:26869702
LegumeIP 2.0--a platform for the study of gene function and genome evolution in legumes. PMID:26578557
Evolutionary Rate Heterogeneity of Primary and Secondary Metabolic Pathway Genes in Arabidopsis thaliana. PMID:26556590
A Journey Through a Leaf: Phenomics Analysis of Leaf Growth in Arabidopsis thaliana. PMID:26217168
Large-Scale Evolutionary Analysis of Genes and Supergene Clusters from Terpenoid Modular Pathways Provides Insights into Metabolic Diversification in Flowering Plants. PMID:26046541
An Ontology-Based GIS for Genomic Data Management of Rumen Microbes. PMID:25873847
Root system markup language: toward a unified root architecture description language. PMID:25614065
A method for increasing expressivity of Gene Ontology annotations using a compositional approach. PMID:24885854
Plant systems biology: insights, advances and challenges. PMID:24671625
Genome-wide binding analysis of the transcription activator ideal plant architecture1 reveals a complex network regulating rice plant architecture. PMID:24170127
Controlled vocabularies for plant anatomical parts optimized for use in data analysis tools and for cross-species studies. PMID:23958387
An integrative, translational approach to understanding rare and orphan genetically based diseases. PMID:23853703
Silicon era of carbon-based life: application of genomics and bioinformatics in crop stress research. PMID:23759993
Maximizing capture of gene co-expression relationships through pre-clustering of input expression samples: an Arabidopsis case study. PMID:23738693
PlantGSEA: a gene set enrichment analysis toolkit for plant community. PMID:23632162
Next-generation phenotyping: requirements and strategies for enhancing our understanding of genotype-phenotype relationships and its relevance to crop improvement. PMID:23471459
The plant ontology as a tool for comparative plant anatomy and genomic analyses. PMID:23220694
Small RNA and transcriptome deep sequencing proffers insight into floral gene regulation in Rosa cultivars. PMID:23171001
Text mining in the biocuration workflow: applications for literature curation at WormBase, dictyBase and TAIR. PMID:23160413
PICARA, an analytical pipeline providing probabilistic inference about a priori candidates genes underlying genome-wide association QTL in plants. PMID:23144785
Ontologies as integrative tools for plant science. PMID:22847540
Uncovering Arabidopsis membrane protein interactome enriched in transporters using mating-based split ubiquitin assays and classification models. PMID:22737156
Multifunctional crop trait ontology for breeders' data: field book, annotation, data discovery and semantic enrichment of the literature. PMID:22476066
Gaining confidence in cross-species annotation transfer: from simple molecular function to complex phenotypic traits. PMID:22319070
MetaCrop 2.0: managing and exploring information about crop plant metabolism. PMID:22086948
Systematic prediction of gene function in Arabidopsis thaliana using a probabilistic functional gene network. PMID:21886106
Computable visually observed phenotype ontological framework for plants. PMID:21702966
PILGRM: an interactive data-driven discovery platform for expert biologists. PMID:21653547
MaizeGDB: curation and outreach go hand-in-hand. PMID:21624896
ARTADE2DB: improved statistical inferences for Arabidopsis gene functions and structure predictions by dynamic structure-based dynamic expression (DSDE) analyses. PMID:21227933
Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana. PMID:21194434
MASCP Gator: an aggregation portal for the visualization of Arabidopsis proteomics data. PMID:21075962
The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources. PMID:21030441
solQTL: a tool for QTL analysis, visualization and linking to genomes at SGN database. PMID:20964836
The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl. PMID:20935049
The teleost anatomy ontology: anatomical representation for the genomics age. PMID:20547776
Applications and methods utilizing the Simple Semantic Web Architecture and Protocol (SSWAP) for bioinformatics resource discovery and disparate data and service integration. PMID:20525377
Gramene QTL database: development, content and applications. PMID:20157478
CORNET: a user-friendly tool for data mining and integration. PMID:20053712
Techniques for integrating -omics data. PMID:19255651
The Protein Feature Ontology: a tool for the unification of protein feature annotations. PMID:18936051
A community-based annotation framework for linking solanaceae genomes with phenomes. PMID:18539779
CressExpress: a tool for large-scale mining of expression data from Arabidopsis. PMID:18467456 -
The plant ontology as a tool for comparative plant anatomy and genomic analyses
PubMed citations: 56.
56 articles citing: The plant ontology as a tool for comparative plant anatomy and genomic analyses
Alleviating Environmental Health Disparities Through Community Science and Data Integration. PMID:35664667
Doing Genetic and Genomic Biology Using the Legume Information System and Associated Resources. PMID:35037201
Transcriptomic Insights on the Preventive Action of Apple (cv Granny Smith) Skin Wounding on Superficial Scald Development. PMID:34948219
A starting guide to root ecology: strengthening ecological concepts and standardising root classification, sampling, processing and trait measurements. PMID:34608637
Computing on Phenotypic Descriptions for Candidate Gene Discovery and Crop Improvement. PMID:33313544
GTRD: an integrated view of transcription regulation. PMID:33231677
The Ontologies Community of Practice: A CGIAR Initiative for Big Data in Agrifood Systems. PMID:33205138
MaizeMine: A Data Mining Warehouse for the Maize Genetics and Genomics Database. PMID:33193550
The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST). PMID:32637990
Automated Methods Enable Direct Computation on Phenotypic Descriptions for Novel Candidate Gene Prediction. PMID:31998331
Cyberinfrastructure and resources to enable an integrative approach to studying forest trees. PMID:31892954
MetaboLights: a resource evolving in response to the needs of its scientific community. PMID:31691833
The Plant Ontology Facilitates Comparisons of Plant Development Stages Across Species. PMID:31214208
Trait ontology analysis based on association mapping studies bridges the gap between crop genomics and Phenomics. PMID:31159731
Integrating herbarium specimen observations into global phenology data systems. PMID:30937223
Modifier Ontologies for frequency, certainty, degree, and coverage phenotype modifier. PMID:30532623
Agronomic Linked Data (AgroLD): A knowledge-based system to enable integrative biology in agronomy. PMID:30500839
The Gene Ontology Resource: 20 years and still GOing strong. PMID:30395331
AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. PMID:30239679
Dealing with multi-source and multi-scale information in plant phenomics: the ontology-driven Phenotyping Hybrid Information System. PMID:30152011
QTLTableMiner++: semantic mining of QTL tables in scientific articles. PMID:29801439
The Plant Phenology Ontology: A New Informatics Resource for Large-Scale Integration of Plant Phenology Data. PMID:29765382
Cross-species multiple environmental stress responses: An integrated approach to identify candidate genes for multiple stress tolerance in sorghum (Sorghum bicolor (L.) Moench) and related model species. PMID:29590108
Bio-SimVerb and Bio-SimLex: wide-coverage evaluation sets of word similarity in biomedicine. PMID:29402212
Ontology-based systematic representation and analysis of traditional Chinese drugs against rheumatism. PMID:29322929
Improving the interoperability of biomedical ontologies with compound alignments. PMID:29316968
Aquilegia B gene homologs promote petaloidy of the sepals and maintenance of the C domain boundary. PMID:29209492
The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics. PMID:29186578
Gramene 2018: unifying comparative genomics and pathway resources for plant research. PMID:29165610
A communal catalogue reveals Earth's multiscale microbial diversity. PMID:29088705
DES-TOMATO: A Knowledge Exploration System Focused On Tomato Species. PMID:28729549
Plant Reactome: a resource for plant pathways and comparative analysis. PMID:27799469
The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability. PMID:27377652
VESPUCCI: Exploring Patterns of Gene Expression in Grapevine. PMID:27242836
Extending gene ontology in the context of extracellular RNA and vesicle communication. PMID:27076901
Emerging semantics to link phenotype and environment. PMID:26713234
Evolutionary Rate Heterogeneity of Primary and Secondary Metabolic Pathway Genes in Arabidopsis thaliana. PMID:26556590
Gramene 2016: comparative plant genomics and pathway resources. PMID:26553803
MaizeGDB update: new tools, data and interface for the maize model organism database. PMID:26432828
Coexpression Network Analysis of Macronutrient Deficiency Response Genes in Rice. PMID:26206757
The Arabidopsis information resource: Making and mining the "gold standard" annotated reference plant genome. PMID:26201819
An ontology approach to comparative phenomics in plants. PMID:25774204
AISO: Annotation of Image Segments with Ontologies. PMID:25584184
POEAS: Automated Plant Phenomic Analysis Using Plant Ontology. PMID:25574136
Finding our way through phenotypes. PMID:25562316
LAILAPS: the plant science search engine. PMID:25480116
Triticeae resources in Ensembl Plants. PMID:25432969
Gene Ontology Consortium: going forward. PMID:25428369
Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology. PMID:25140222
Ontology for the asexual development and anatomy of the colonial chordate Botryllus schlosseri. PMID:24789338
RARGE II: an integrated phenotype database of Arabidopsis mutant traits using a controlled vocabulary. PMID:24272250
MEGANTE: a web-based system for integrated plant genome annotation. PMID:24253915
Manually curated database of rice proteins. PMID:24214963
Anatomical entity mention recognition at literature scale. PMID:24162468
The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments. PMID:24093723
Controlled vocabularies for plant anatomical parts optimized for use in data analysis tools and for cross-species studies. PMID:23958387 -
Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and Growth Stages
PubMed citations: 55.
55 articles citing: Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and Growth Stages
Genetic Diversity of Transcription Factor Genes in Triticum and Mining for Promising Haplotypes for Beneficial Agronomic Traits. PMID:35873966
Genetic and Genomic Resources for Soybean Breeding Research. PMID:35567182
A COMPASS for VESPUCCI: A FAIR Way to Explore the Grapevine Transcriptomic Landscape. PMID:35283898
Opportunities and limits of controlled-environment plant phenotyping for climate response traits. PMID:34302493
Challenges for FAIR-compliant description and comparison of crop phenotype data with standardized controlled vocabularies. PMID:33991093
GMO Genetic Elements Thesaurus (GMO-GET): a controlled vocabulary for the consensus designation of introduced or modified genetic elements in genetically modified organisms. PMID:33546585
Towards semantic interoperability: finding and repairing hidden contradictions in biomedical ontologies. PMID:33319712
Enabling reusability of plant phenomic datasets with MIAPPE 1.1. PMID:32171029
Formal axioms in biomedical ontologies improve analysis and interpretation of associated data. PMID:31821406
Fruit Salad in the Lab: Comparing Botanical Species to Help Deciphering Fruit Primary Metabolism. PMID:31354750
Cyberinfrastructure to Improve Forest Health and Productivity: The Role of Tree Databases in Connecting Genomes, Phenomes, and the Environment. PMID:31293610
Trait ontology analysis based on association mapping studies bridges the gap between crop genomics and Phenomics. PMID:31159731
It's Hard to Avoid Avoidance: Uncoupling the Evolutionary Connection between Plant Growth, Productivity and Stress "Tolerance". PMID:30463352
Plant data visualisation using network graphs. PMID:30186704
Extraction of phenotypic traits from taxonomic descriptions for the tree of life using natural language processing. PMID:29732265
The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics. PMID:29186578
AtPID: a genome-scale resource for genotype-phenotype associations in Arabidopsis. PMID:27899679
MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions. PMID:27076900
LEAFDATA: a literature-curated database for Arabidopsis leaf development. PMID:26884807
Translational genomics for plant breeding with the genome sequence explosion. PMID:26269219
The Arabidopsis information resource: Making and mining the "gold standard" annotated reference plant genome. PMID:26201819
Large-Scale Evolutionary Analysis of Genes and Supergene Clusters from Terpenoid Modular Pathways Provides Insights into Metabolic Diversification in Flowering Plants. PMID:26046541
A software tool for the input and management of phenotypic data using personal digital assistants and other mobile devices. PMID:25866550
From ontology to semantic similarity: calculation of ontology-based semantic similarity. PMID:23533360
Next-generation phenotyping: requirements and strategies for enhancing our understanding of genotype-phenotype relationships and its relevance to crop improvement. PMID:23471459
Building an efficient curation workflow for the Arabidopsis literature corpus. PMID:23221298
The plant ontology as a tool for comparative plant anatomy and genomic analyses. PMID:23220694
H2DB: a heritability database across multiple species by annotating trait-associated genomic loci. PMID:23193255
Small RNA and transcriptome deep sequencing proffers insight into floral gene regulation in Rosa cultivars. PMID:23171001
Developing a biocuration workflow for AgBase, a non-model organism database. PMID:23160411
Jointly creating digital abstracts: dealing with synonymy and polysemy. PMID:23110757
Assessment of community-submitted ontology annotations from a novel database-journal partnership. PMID:22859749
AraPath: a knowledgebase for pathway analysis in Arabidopsis. PMID:22760305
The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. PMID:22140109
Computable visually observed phenotype ontological framework for plants. PMID:21702966
Semantic-JSON: a lightweight web service interface for Semantic Web contents integrating multiple life science databases. PMID:21632604
Multi-source and ontology-based retrieval engine for maize mutant phenotypes. PMID:21558151
ONTO-ToolKit: enabling bio-ontology engineering via Galaxy. PMID:21210987
Gramene database in 2010: updates and extensions. PMID:21076153
AgBase: supporting functional modeling in agricultural organisms. PMID:21075795
AtPID: the overall hierarchical functional protein interaction network interface and analytic platform for Arabidopsis. PMID:21036873
High throughput generation of promoter reporter (GFP) transgenic lines of low expressing genes in Arabidopsis and analysis of their expression patterns. PMID:20687964
The teleost anatomy ontology: anatomical representation for the genomics age. PMID:20547776
A MOD(ern) perspective on literature curation. PMID:20221640
Probing the reproducibility of leaf growth and molecular phenotypes: a comparison of three Arabidopsis accessions cultivated in ten laboratories. PMID:20200072
Web-queryable large-scale data sets for hypothesis generation in plant biology. PMID:19401381
TreeGenes: A forest tree genome database. PMID:18725987
UTILLdb, a Pisum sativum in silico forward and reverse genetics tool. PMID:18302733
The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations. PMID:18194960
Oryza Tag Line, a phenotypic mutant database for the Genoplante rice insertion line library. PMID:17947330
MetaCrop: a detailed database of crop plant metabolism. PMID:17933764
AlzPharm: integration of neurodegeneration data using RDF. PMID:17493287
MaizeGDB's new data types, resources and activities. PMID:17202174
The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant. PMID:17142475
Whole-plant growth stage ontology for angiosperms and its application in plant biology. PMID:16905665 -
The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics
PubMed citations: 44.
44 articles citing: The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics
First Plant Cell Atlas symposium report. PMID:35774620
Phenotypic Variation and the Impact of Admixture in the Oryza rufipogon Species Complex (ORSC). PMID:35769295
Alleviating Environmental Health Disparities Through Community Science and Data Integration. PMID:35664667
Data standardization of plant-pollinator interactions. PMID:35639882
GrainGenes: a data-rich repository for small grains genetics and genomics. PMID:35616118
Genetic and Genomic Resources for Soybean Breeding Research. PMID:35567182
DIVIS: a semantic DIstance to improve the VISualisation of heterogeneous phenotypic datasets. PMID:35379292
Plant Reactome and PubChem: The Plant Pathway and (Bio)Chemical Entity Knowledgebases. PMID:35037224
CottonGen: The Community Database for Cotton Genomics, Genetics, and Breeding Research. PMID:34961276
Integrating Genomic and Phenomic Approaches to Support Plant Genetic Resources Conservation and Use. PMID:34834625
PlantGSAD: a comprehensive gene set annotation database for plant species. PMID:34534340
Arabidopsis Coexpression Tool: a tool for gene coexpression analysis in Arabidopsis thaliana. PMID:34381973
Scaling up high-throughput phenotyping for abiotic stress selection in the field. PMID:34076731
Crop breeding for a changing climate: integrating phenomics and genomics with bioinformatics. PMID:33852055
Editorial: Phenotyping; From Plant, to Data, to Impact and Highlights of the International Plant Phenotyping Symposium - IPPS 2018. PMID:33343612
Towards semantic interoperability: finding and repairing hidden contradictions in biomedical ontologies. PMID:33319712
Hierarchical Canonical Correlation Analysis Reveals Phenotype, Genotype, and Geoclimate Associations in Plants. PMID:33313545
Computing on Phenotypic Descriptions for Candidate Gene Discovery and Crop Improvement. PMID:33313544
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
The Ontologies Community of Practice: A CGIAR Initiative for Big Data in Agrifood Systems. PMID:33205138
Gramene 2021: harnessing the power of comparative genomics and pathways for plant research. PMID:33170273
Enabling a fast annotation process with the Table2Annotation tool. PMID:32634873
WTO, an ontology for wheat traits and phenotypes in scientific publications. PMID:32634868
A Physio-Morphological Trait-Based Approach for Breeding Drought Tolerant Wheat. PMID:32582249
Phenomics-based GWAS analysis reveals the genetic architecture for drought resistance in cotton. PMID:32558152
Enabling reusability of plant phenomic datasets with MIAPPE 1.1. PMID:32171029
Cyberinfrastructure and resources to enable an integrative approach to studying forest trees. PMID:31892954
Plant Reactome: a knowledgebase and resource for comparative pathway analysis. PMID:31680153
MBKbase for rice: an integrated omics knowledgebase for molecular breeding in rice. PMID:31624841
GWAS Atlas: a curated resource of genome-wide variant-trait associations in plants and animals. PMID:31566222
Cyberinfrastructure to Improve Forest Health and Productivity: The Role of Tree Databases in Connecting Genomes, Phenomes, and the Environment. PMID:31293610
The Plant Ontology Facilitates Comparisons of Plant Development Stages Across Species. PMID:31214208
Small RNA-seq reveals novel regulatory components for apomixis in Paspalum notatum. PMID:31195966
Review: New sensors and data-driven approaches-A path to next generation phenomics. PMID:31003608
BrAPI-an application programming interface for plant breeding applications. PMID:30903186
Involving community in genes and pathway curation. PMID:30649295
Computer vision-based phenotyping for improvement of plant productivity: a machine learning perspective. PMID:30520975
Computational aspects underlying genome to phenome analysis in plants. PMID:30500991
Agronomic Linked Data (AgroLD): A knowledge-based system to enable integrative biology in agronomy. PMID:30500839
15 years of GDR: New data and functionality in the Genome Database for Rosaceae. PMID:30357347
AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. PMID:30239679
Growing and cultivating the forest genomics database, TreeGenes. PMID:30239664
Dealing with multi-source and multi-scale information in plant phenomics: the ontology-driven Phenotyping Hybrid Information System. PMID:30152011 -
The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant
PubMed citations: 37.
37 articles citing: The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant
Vision, challenges and opportunities for a Plant Cell Atlas. PMID:34491200
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
Dealing with multi-source and multi-scale information in plant phenomics: the ontology-driven Phenotyping Hybrid Information System. PMID:30152011
The Quantitative Genetic Control of Root Architecture in Maize. PMID:30020530
Cross-species multiple environmental stress responses: An integrated approach to identify candidate genes for multiple stress tolerance in sorghum (Sorghum bicolor (L.) Moench) and related model species. PMID:29590108
The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics. PMID:29186578
Reshaping Plant Biology: Qualitative and Quantitative Descriptors for Plant Morphology. PMID:28217137
Towards an open grapevine information system. PMID:27917288
A Journey Through a Leaf: Phenomics Analysis of Leaf Growth in Arabidopsis thaliana. PMID:26217168
Image-based phenotyping of plant disease symptoms. PMID:25601871
An ontology for microbial phenotypes. PMID:25433798
Elucidating gene function and function evolution through comparison of co-expression networks of plants. PMID:25191328
Genomics and bioinformatics resources for translational science in Rosaceae. PMID:24634697
Integration of root phenes for soil resource acquisition. PMID:24062755
Controlled vocabularies for plant anatomical parts optimized for use in data analysis tools and for cross-species studies. PMID:23958387
The plant ontology as a tool for comparative plant anatomy and genomic analyses. PMID:23220694
DcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more. PMID:23161684
Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models. PMID:23033316
Ontologies as integrative tools for plant science. PMID:22847540
Multifunctional crop trait ontology for breeders' data: field book, annotation, data discovery and semantic enrichment of the literature. PMID:22476066
Uberon, an integrative multi-species anatomy ontology. PMID:22293552
Computable visually observed phenotype ontological framework for plants. PMID:21702966
PHENOPSIS DB: an information system for Arabidopsis thaliana phenotypic data in an environmental context. PMID:21554668
The teleost anatomy ontology: anatomical representation for the genomics age. PMID:20547776
Gramene QTL database: development, content and applications. PMID:20157478
CORNET: a user-friendly tool for data mining and integration. PMID:20053712
Web-queryable large-scale data sets for hypothesis generation in plant biology. PMID:19401381
MaizeGDB: The maize model organism database for basic, translational, and applied research. PMID:18769488
A plant resource and experiment management system based on the Golm Plant Database as a basic tool for omics research. PMID:18495032
UTILLdb, a Pisum sativum in silico forward and reverse genetics tool. PMID:18302733
Animal trait ontology: The importance and usefulness of a unified trait vocabulary for animal species. PMID:18272850
The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations. PMID:18194960
PlantTribes: a gene and gene family resource for comparative genomics in plants. PMID:18073194
Oryza Tag Line, a phenotypic mutant database for the Genoplante rice insertion line library. PMID:17947330
GDR (Genome Database for Rosaceae): integrated web-database for Rosaceae genomics and genetics data. PMID:17932055
A rice phenomics study--phenotype scoring and seed propagation of a T-DNA insertion-induced rice mutant population. PMID:17701278 -
Ontologies as integrative tools for plant science
PubMed citations: 28.
28 articles citing: Ontologies as integrative tools for plant science
DIVIS: a semantic DIstance to improve the VISualisation of heterogeneous phenotypic datasets. PMID:35379292
RapGreen, an interactive software and web package to explore and analyze phylogenetic trees. PMID:34568824
Challenges for FAIR-compliant description and comparison of crop phenotype data with standardized controlled vocabularies. PMID:33991093
The Ontologies Community of Practice: A CGIAR Initiative for Big Data in Agrifood Systems. PMID:33205138
Developing a scalable FHIR-based clinical data normalization pipeline for standardizing and integrating unstructured and structured electronic health record data. PMID:32025655
The Plant Ontology Facilitates Comparisons of Plant Development Stages Across Species. PMID:31214208
Plant data visualisation using network graphs. PMID:30186704
Dealing with multi-source and multi-scale information in plant phenomics: the ontology-driven Phenotyping Hybrid Information System. PMID:30152011
QTLTableMiner++: semantic mining of QTL tables in scientific articles. PMID:29801439
Bio-SimVerb and Bio-SimLex: wide-coverage evaluation sets of word similarity in biomedicine. PMID:29402212
Automated Integration of Trees and Traits: A Case Study Using Paired Fin Loss Across Teleost Fishes. PMID:29325126
The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics. PMID:29186578
DES-TOMATO: A Knowledge Exploration System Focused On Tomato Species. PMID:28729549
The anatomy of phenotype ontologies: principles, properties and applications. PMID:28387809
The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants. PMID:27842607
Behavior change interventions: the potential of ontologies for advancing science and practice. PMID:27481101
An ontology approach to comparative phenomics in plants. PMID:25774204
The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology. PMID:25276334
Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology. PMID:25140222
Field-omics-understanding large-scale molecular data from field crops. PMID:24999347
RARGE II: an integrated phenotype database of Arabidopsis mutant traits using a controlled vocabulary. PMID:24272250
Manually curated database of rice proteins. PMID:24214963
In silico approaches and the role of ontologies in aging research. PMID:24188080
Where have all the crop phenotypes gone? PMID:23824246
A semantic model for species description applied to the ensign wasps (hymenoptera: evaniidae) of New Caledonia. PMID:23652347
The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies. PMID:23398680
The plant ontology as a tool for comparative plant anatomy and genomic analyses. PMID:23220694
Gene Ontology annotations and resources. PMID:23161678 -
Whole-plant growth stage ontology for angiosperms and its application in plant biology
PubMed citations: 21.
21 articles citing: Whole-plant growth stage ontology for angiosperms and its application in plant biology
The hidden half comes into the spotlight: Peeking inside the black box of root developmental phases. PMID:35059627
Distinct Metabolome Changes during Seed Germination of Lettuce (Lactuca sativa L.) in Response to Thermal Stress as Revealed by Untargeted Metabolomics Analysis. PMID:32098243
The Plant Ontology Facilitates Comparisons of Plant Development Stages Across Species. PMID:31214208
Trait ontology analysis based on association mapping studies bridges the gap between crop genomics and Phenomics. PMID:31159731
Rapid genotype "independent" Zea mays L. (maize) transformation via direct somatic embryogenesis. PMID:29780216
Cross-species multiple environmental stress responses: An integrated approach to identify candidate genes for multiple stress tolerance in sorghum (Sorghum bicolor (L.) Moench) and related model species. PMID:29590108
The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics. PMID:29186578
Adaptive evolution of seed oil content in angiosperms: accounting for the global patterns of seed oils. PMID:27613109
Genome-wide binding analysis of the transcription activator ideal plant architecture1 reveals a complex network regulating rice plant architecture. PMID:24170127
From manual curation to visualization of gene families and networks across Solanaceae plant species. PMID:23681907
The plant ontology as a tool for comparative plant anatomy and genomic analyses. PMID:23220694
Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models. PMID:23033316
Ontologies as integrative tools for plant science. PMID:22847540
The Arabidopsis CstF64-Like RSR1/ESP1 Protein Participates in Glucose Signaling and Flowering Time Control. PMID:22629280
Computable visually observed phenotype ontological framework for plants. PMID:21702966
Gramene QTL database: development, content and applications. PMID:20157478
CORNET: a user-friendly tool for data mining and integration. PMID:20053712
The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations. PMID:18194960
PlantTribes: a gene and gene family resource for comparative genomics in plants. PMID:18073194
Oryza Tag Line, a phenotypic mutant database for the Genoplante rice insertion line library. PMID:17947330
The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant. PMID:17142475 -
Biological ontologies in rice databases. An introduction to the activities in Gramene and Oryzabase
PubMed citations: 19.
19 articles citing: Biological ontologies in rice databases. An introduction to the activities in Gramene and Oryzabase
The Plant Ontology Facilitates Comparisons of Plant Development Stages Across Species. PMID:31214208
A genome scale metabolic network for rice and accompanying analysis of tryptophan, auxin and serotonin biosynthesis regulation under biotic stress. PMID:24280345
The plant ontology as a tool for comparative plant anatomy and genomic analyses. PMID:23220694
Ontology-based cross-species integration and analysis of Saccharomyces cerevisiae phenotypes. PMID:23046642
Ontologies as integrative tools for plant science. PMID:22847540
Computational tools for comparative phenomics: the role and promise of ontologies. PMID:22814867
GrameneMart: the BioMart data portal for the Gramene project. PMID:22374386
TNAURice: Database on rice varieties released from Tamil Nadu Agricultural University. PMID:21364829
Worm Phenotype Ontology: integrating phenotype data within and beyond the C. elegans community. PMID:21261995
Gramene database in 2010: updates and extensions. PMID:21076153
Integrating phenotype ontologies across multiple species. PMID:20064205
Orymold: ontology based gene expression data integration and analysis tool applied to rice. PMID:19463186
Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and Growth Stages. PMID:18629207
The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations. PMID:18194960
A rice phenomics study--phenotype scoring and seed propagation of a T-DNA insertion-induced rice mutant population. PMID:17701278
The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant. PMID:17142475
Development of a controlled vocabulary and software application to analyze fruit shape variation in tomato and other plant species. PMID:16684933
Oryzabase. An integrated biological and genome information database for rice. PMID:16403737
Gramene: a bird's eye view of cereal genomes. PMID:16381966 -
An ontology approach to comparative phenomics in plants
PubMed citations: 16.
16 articles citing: An ontology approach to comparative phenomics in plants
Transforming the study of organisms: Phenomic data models and knowledge bases. PMID:33232313
Emerging Technologies in Algal Biotechnology: Toward the Establishment of a Sustainable, Algae-Based Bioeconomy. PMID:32256509
A Pan-plant Protein Complex Map Reveals Deep Conservation and Novel Assemblies. PMID:32191846
Automated Methods Enable Direct Computation on Phenotypic Descriptions for Novel Candidate Gene Prediction. PMID:31998331
Global agricultural concept space: lightweight semantics for pragmatic interoperability. PMID:31552293
Evolutionary characteristics of intergenic transcribed regions indicate rare novel genes and widespread noisy transcription in the Poaceae. PMID:31431676
The Plant Ontology Facilitates Comparisons of Plant Development Stages Across Species. PMID:31214208
Trait ontology analysis based on association mapping studies bridges the gap between crop genomics and Phenomics. PMID:31159731
Agronomic Linked Data (AgroLD): A knowledge-based system to enable integrative biology in agronomy. PMID:30500839
The Next Generation of Training for Arabidopsis Researchers: Bioinformatics and Quantitative Biology. PMID:29208732
The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics. PMID:29186578
Morphological phenotyping and genetic analyses of a new chemical-mutagenized population of tobacco (Nicotiana tabacum L.). PMID:28401357
The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants. PMID:27842607
The Quest for Understanding Phenotypic Variation via Integrated Approaches in the Field Environment. PMID:27482076
Emerging semantics to link phenotype and environment. PMID:26713234
MaizeGDB update: new tools, data and interface for the maize model organism database. PMID:26432828 -
The Plant Ontology: A Tool for Plant Genomics
PubMed citations: 10.
10 articles citing: The Plant Ontology: A Tool for Plant Genomics
Expression Atlas update: gene and protein expression in multiple species. PMID:34850121
Applying FAIR Principles to Plant Phenotypic Data Management in GnpIS. PMID:33313522
Experiment design driven FAIRification of omics data matrices, an exemplar. PMID:31831744
Trait ontology analysis based on association mapping studies bridges the gap between crop genomics and Phenomics. PMID:31159731
AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. PMID:30239679
Extraction of phenotypic traits from taxonomic descriptions for the tree of life using natural language processing. PMID:29732265
An Updated Functional Annotation of Protein-Coding Genes in the Cucumber Genome. PMID:29599790
The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics. PMID:29186578
Gramene 2018: unifying comparative genomics and pathway resources for plant research. PMID:29165610
Reshaping Plant Biology: Qualitative and Quantitative Descriptors for Plant Morphology. PMID:28217137 -
AISO: Annotation of Image Segments with Ontologies
PubMed citations: 5.
5 articles citing: AISO: Annotation of Image Segments with Ontologies
The Plant Ontology Facilitates Comparisons of Plant Development Stages Across Species. PMID:31214208
The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics. PMID:29186578
PhenoImageShare: an image annotation and query infrastructure. PMID:27267125
Biomedical imaging ontologies: A survey and proposal for future work. PMID:26167381
The role of ontologies in biological and biomedical research: a functional perspective. PMID:25863278 - http://dx.doi.org/10.1093/nar/gkx1152
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gene
metasource: Fairsharing.org
version: FAIRsharing.org: Planteome; Planteome; DOI: https://doi.org/10.25504/FAIRsharing.k0kcjw; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
gene ontology enrichment
metasource: Fairsharing.org
version: FAIRsharing.org: Planteome; Planteome; DOI: https://doi.org/10.25504/FAIRsharing.k0kcjw; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
gene functional annotation
metasource: Fairsharing.org
version: FAIRsharing.org: Planteome; Planteome; DOI: https://doi.org/10.25504/FAIRsharing.k0kcjw; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
genome annotation
metasource: Fairsharing.org
version: FAIRsharing.org: Planteome; Planteome; DOI: https://doi.org/10.25504/FAIRsharing.k0kcjw; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
germplasm
metasource: Fairsharing.org
version: FAIRsharing.org: Planteome; Planteome; DOI: https://doi.org/10.25504/FAIRsharing.k0kcjw; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
phenotype
metasource: Fairsharing.org
version: FAIRsharing.org: Planteome; Planteome; DOI: https://doi.org/10.25504/FAIRsharing.k0kcjw; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
quantitative trait loci
metasource: Fairsharing.org
version: FAIRsharing.org: Planteome; Planteome; DOI: https://doi.org/10.25504/FAIRsharing.k0kcjw; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
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More detailed information about this field from each metasource.
gene
metasource: Fairsharing.orgversion: FAIRsharing.org: Planteome; Planteome; DOI: https://doi.org/10.25504/FAIRsharing.k0kcjw; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
gene ontology enrichment
metasource: Fairsharing.orgversion: FAIRsharing.org: Planteome; Planteome; DOI: https://doi.org/10.25504/FAIRsharing.k0kcjw; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
gene functional annotation
metasource: Fairsharing.orgversion: FAIRsharing.org: Planteome; Planteome; DOI: https://doi.org/10.25504/FAIRsharing.k0kcjw; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
genome annotation
metasource: Fairsharing.orgversion: FAIRsharing.org: Planteome; Planteome; DOI: https://doi.org/10.25504/FAIRsharing.k0kcjw; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
germplasm
metasource: Fairsharing.orgversion: FAIRsharing.org: Planteome; Planteome; DOI: https://doi.org/10.25504/FAIRsharing.k0kcjw; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
phenotype
metasource: Fairsharing.orgversion: FAIRsharing.org: Planteome; Planteome; DOI: https://doi.org/10.25504/FAIRsharing.k0kcjw; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
quantitative trait loci
metasource: Fairsharing.orgversion: FAIRsharing.org: Planteome; Planteome; DOI: https://doi.org/10.25504/FAIRsharing.k0kcjw; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
gene gene ontology enrichment gene functional annotation genome annotation germplasm phenotype quantitative trait loci
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