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Planteome database
Gathers a suite of interconnected reference ontologies. Planteome database’s terminologies are employed for the annotation of plant gene expression data, traits, phenotypes, genomes and germplasm, across 95 plant taxa. It contains species-specific Crop Ontologies (CO) and phenotype scoring standards. This database can assist in identification of traits of interest, and locates data, including germplasm, quantitative trait locus (QTL) and genes associated with a given trait.
A tomato mutant database providing visible phenotypic data of tomato mutant lines generated by ethylmethane sulfonate (EMS) treatment or gamma-ray irradiation in the genetic background of Micro-Tom, a small and rapidly growing variety. In the updated version of TOMATOMA, additional EMS mutant lines were generated via a second round of EMS treatment to increase the mutation frequency, and a bulk set of mutant seeds was prepared for screening. Furthermore, we collected additional information concerning Brix values and carotenoid contents in mutant fruits for TOMATOMA. This metabolite information is valuable for both basic and applied tomato research.
Holds a diverse variety of data types, ranging from molecular to phenotypic, and allows researchers to perform query between such data for any plant species. GERMINATE aims to inform users on genetic and phenotypic topics and can be used for any type of genetic system. It offers different features: (1) it is Multi-Crop Passport Descriptors (MCPD) compatible; (2) it permits visualization driven; (3) users can customize the interface; and (4) data can be exported in several formats.
SesameFG / Sesame Functional Genomics Database
Promotes sesame functional genomics research. SesameFG is an integrated repository of comprehensive genotype-phenotype information that provides comprehensive genetic information, phenotypic information and bioinformatics analysis for Sesamum indicum L. functional genomics research. It was constructed using large-scale genetic and phenotypic sesame resources that came from public databases, literature, and sesame functional genomics consortium inputs.
A database of salt-tolerant plants-halophytes. Records of plant species tolerant of salt concentrations of around 80 mM sodium chloride or more have been collected, along with data on plant type, life form, ecotypes, maximum salinity tolerated, the presence or absence of salt glands, photosynthetic pathway, antioxidants, secondary metabolites, compatible solutes, habitat, economic use and whether there are publications on germination, microbial interactions and mycorrhizal status, bioremediation and of molecular data. eHALOPH can be used in the analysis of traits associated with tolerance and for informing choice of species that might be used for saline agriculture, bioremediation or ecological restoration and rehabilitation of degraded wetlands or other areas.
Optimas-DW / OPTIMAS Data Warehouse
A comprehensive data collection for maize. Optimas-DW integrates data from different data domains such as transcriptomics, metabolomics, ionomics, proteomics and phenomics. A web interface allows users to browse through all stored experiment data in OPTIMAS-DW including all data domains. Furthermore, the user can filter the data to extract information of particular interest. All data can be exported into different file formats for further data analysis and visualisation. The data analysis integrates data from different data domains and enables the user to find answers to different systems biology questions. Finally, maize specific pathway information is provided.
GnpIS / Genoplante Information System
A multispecies integrative information system dedicated to plant and fungi pests. GnpIS bridges genetic and genomic data, allowing researchers access to both genetic information (e.g. genetic maps, quantitative trait loci, markers, single nucleotide polymorphisms, germplasms and genotypes) and genomic data (e.g. genomic sequences, physical maps, genome annotation and expression data) for species of agronomical interest. GnpIS is used by both large international projects and plant science departments at the French National Institute for Agricultural Research.
PGP / Plant Genomics and Phenomics Research Data Repository
An infrastructure to comprehensively publish plant research data. PGP covers in particular cross-domain datasets that are not being published in central repositories because of its volume or unsupported data scope, like image collections from plant phenotyping and microscopy, unfinished genomes, genotyping data, visualizations of morphological plant models, data from mass spectrometry as well as software and documents. After an internal review process, data are published as citable digital object identifiers and a core set of technical metadata is registered at DataCite. The repository uses e!DAL as software infrastructure and a Hierarchical Storage Management System as data archival backend.