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GreenPhylDB is a database designed for comparative and functional genomics based on complete genomes. Version 2 now contains sixteen full genomes of members of the plantae kingdom, ranging from algae to angiosperms, automatically clustered into gene families. Gene families are manually annotated and then analyzed phylogenetically in order to elucidate(More)
To address biodiversity issues in ecology and assess the consequences of ecosystem changes, large quantities of long-term observational data from multiple data sets need to be integrated and characterized in a unified way. During these last decades, functional trait-based approaches have shown great potential to facilitate the understanding and the(More)
— The Planteome project is a centralized online plant informatics portal which provides semantic integration of widely diverse datasets with the goal of plant improvement. Traditional plant breeding methods for crop improvement may be combined with next-generation analysis methods and automated scoring of traits and phenotypes to develop improved varieties.(More)
— Addressing global challenges to agricultural productivity and profitability increasingly requires access to data from a variety of disciplines, and the ability to easily combine and analyze related data sets. Innovation in agricultural research for development must therefore be mediated by reliable and consistently annotated information resources across(More)
— An expected use case of plant phenotype ontologies will be the identification of germplasm containing particular traits of interest. If phenotype data from experiments is annotated using ontologies, it makes sense to include annotations to that germplasm source. A lack of standardized data formatting reduces the utility of these data. Standardizing(More)
—Crop specific ontologies for phenotype annotations in breeding have proliferated over the last 10 years. Across-crop data interoperability involves linking those ontologies together. For this purpose, the Planteome project is mapping the Crop Ontology traits (www.cropontology.org) to the reference ontology for plant traits, Trait Ontology (TO). Manual(More)
To address biodiversity issues in ecology and to assess the consequences of ecosystem changes, large quantities of long-term observational data from multiple datasets need to be integrated and characterized in a unified way. Linked open data initiatives in ecology aim at promoting and sharing such observational data at the web-scale. Here we present a web(More)
Soil invertebrates are known to be much involved in soil behaviour and therefore in the provision of ecosystem services. Functional trait-based approaches are methodologies which can be used to understand soil invertebrates' responses to their environment. They (i) improve the predictions and (ii) are less dependent on space and time. The way traits have(More)
Molecular biologists, just like geneticists, make use of various experimental mechanisms and devices to conduct research and to validate or invalidate their theories or initial hypotheses. Mechanisms powered by information technology, called in silico, put data and analysis tools at the centre of the experiments, and are thus different from in vivo, ex vivo(More)