Gathers genomic, genetic and phenotypic information about tropical crops. TropGeneDB is an online repository that can record crop information on molecular markers, quantitative trait loci (QTL), genetic and physical maps, genotyping and phenotyping studies, and on genetic resources. It can record information on: genetic diversity, association and linkage disequilibrium (LD) studies, geographic origin, parentage, collection, or ecology.
Retrieves plant genomic data in a phenotypic attributes context. LAILAPS provides a web browser establishing links to more than 15 databases that indexes over 60 million of documents. This program includes a system for query assistance, an evidence-based annotation system and, additionally, an algorithm allowing users to perform open search corpus-based queries. It can also be installed locally for customized researches.
An integrated phenotype database of Arabidopsis mutant traits using a controlled vocabulary. RARGE integrates the phenotypes of four Arabidopsis mutant lines (including two loss-of-function and two gain-of-function lines) by mapping descriptions into PO and PATO. RARGE is an updated version of the RIKEN Arabidopsis Genome Encyclopedia (RARGE), a database of fl-cDNAs and Ds transposon mutant lines.
Provides a central repository of population-scale phenotypes for A. thaliana inbred lines. AraPheno includes various features to easily access, download and visualize the phenotypic data. This will facilitate a comparative analysis of the many different types of phenotypic data, which is the base to further enhance our understanding of the genotype–phenotype map.
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.
Allows to search phenotypic data in transposon-insertional mutants. RAPID permits to browse through 4000 transposon-insertional lines and to examine visible phenotypes systematically at each growth stage. Many mutant phenotypes can be search and are classified into phenotypic categories. All data and images have been presents into the database which concerns transposon-insertional lines on the Arabidopsis genome.
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.
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.
Hosts information dealing with Daucus carota L. CarrotDB gathers produced carrot draft genome, putative genes and coding sequences. This repository also supplies information related to simple sequence repeats (SSRs) with specific primers, predicted transcription factors (TFs), and transcript sequences as well as utilities derived from Genome Map and BLAST. The database can also be browsed from the ApiaceaeDatabase.
Assists rice geneticists and breeders to find and utilize agronomically useful genes. IWR Database provides a source of information about a large number of wild rice accessions collected from different agro-climatic zones of India. It includes wild rice accessions together with information on their salinity and drought tolerance phenotype. The accessions have been characterized based on morphological characters and molecular markers.
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.
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.
Consists of a hyperspectral database about over 40 fruits and vegetables. Giessen's hyperspectral images of fruits and vegetables database contains a set of functions for opening and manipulating the hyperspectral images in MATLAB. It furnishes images taken under controlled lighting conditions using a stabilized, broadband illuminant located near the daylight locus.
Links species with traits and reference information about data source, location, habitat and trait measurement protocol. LEDA Traitbase contains a synonymized plant list at the specie level, completed with authorities. It encompasses the whole range of functional ecology and phylogenetic ecology, the fusion of ecology and evolutionary history. This database is useful for studying distribution patterns of rarity and endangerment of plant species.
Contains information of the phenotype of about genomic sequences of the T-DNA insertion sites and 500 morphological mutants. RIKEN Arabidopsis Activation tagging line includes more than 50,000 RIKEN Activation Tagging lines. Several mutant phenotypes are handle and store in various categories. It is possible users to search information by different classes and to download contents.
Gathers information about agricultural studies. GARDIAN offers a platform which compiles publications and metrics linked to the Consultative Group on International Agricultural Research (CGIAR) areas of research. It gives access to more than 93000 publications including reports and working papers as well as over 2300 datasets. The research tool points towards a panel providing publications, datasets and genetic accession related to a subject of interest.
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