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The MetaCrop resource contains information on the major metabolic pathways mainly in crops of agricultural and economic importance. The database includes manually curated information on reactions and the kinetic data associated with these reactions. Ontology terms are used and publication identification available to ease mining the data.
The Arabidopsis Information Resource
The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana.
Golm Metabolome Database
The Golm Metabolome Database (GMD) provides gas chromatography (GC) mass spectrometry (MS) reference spectra, reference metabolite profiles and tools for one of the most widespread routine technologies applied to the large scale screening and discovery of novel metabolic biomarkers.
Nottingham Arabidopsis Stock Centre Seeds Database
The Nottingham Arabidopsis Stock Centre (NASC) provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community.
Gramene, a comparative mapping resource for grains
Gramene's purpose is to provide added value to data sets available within the public sector, which will facilitate researchers' ability to understand the grass genomes and take advantage of genomic sequence known in one species for identifying and understanding corresponding genes, pathways and phenotypes in other grass species.
The Oryzabase is a comprehensive rice science database established in 2000 by rice researcher's committee in Japan. The Oryzabase consists of five parts, (1) genetic resource stock information, (2) gene dictionary, (3) chromosome maps, (4) mutant images, and (5) fundamental knowledge of rice science.
Genome Database for Rosaceae
The Genome Database for Rosaceae (GDR) is a curated and integrated web-based relational database providing centralized access to Rosaceae genomics and genetics data and analysis tools to facilitate cross-species utilization of data.
Manually Curated Database of Rice Proteins
‘Manually Curated Database of Rice Proteins’ (MCDRP) is a unique manually curated database based on published experimental data. Currently, the database has data for over 1800 rice proteins curated from > 4000 different experiments of over 400 research articles. Since every aspect of the experiment such as gene name, plant type, tissue and developmental stage has been digitized, experimental data can be rapidly accessed and integrated.
Genetic and Genomic Information System
GnpIS is a multispecies integrative information system dedicated to plant and fungi pests. It bridges genetic and genomic data, allowing researchers access to both genetic information (e.g. genetic maps, quantitative trait loci, association genetics, markers, polymorphisms, germplasms, phenotypes 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. It is regularly improved and released several times per year. GnpIS is accessible through a web portal and allows to browse different types of data either independently through dedicated interfaces or simultaneously using a quick search ('google like search') or advanced search (Biomart, Galaxy, Intermine) tools.
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0822201 (US National Science Foundation (NSF))
1127112 (US National Science Foundation (NSF))
Finding our way through phenotypes
Deans AR,Lewis SE,Huala E,Anzaldo SS,Ashburner M,Balhoff JP,Blackburn DC,Blake JA,Burleigh JG,Chanet B,Cooper LD,Courtot M,Csosz S,Cui H,Dahdul W,Das S,Dececchi TA,Dettai A,Diogo R,Druzinsky RE,Dumontier M,Franz NM,Friedrich F,Gkoutos GV,Haendel M,Harmon LJ,Hayamizu TF,He Y,Hines HM,Ibrahim N,Jackson LM,Jaiswal P,James-Zorn C,Kohler S,Lecointre G,Lapp H,Lawrence CJ,Le Novere N,Lundberg JG,Macklin J,Mast AR,Midford PE,Miko I,Mungall CJ,Oellrich A,Osumi-Sutherland D,Parkinson H,Ramirez MJ,Richter S,Robinson PN,Ruttenberg A,Schulz KS,Segerdell E,Seltmann KC,Sharkey MJ,Smith AD,Smith B,Specht CD,Squires RB,Thacker RW,Thessen A,Fernandez-Triana J,Vihinen M,Vize PD,Vogt L,Wall CE,Walls RL,Westerfeld M,Wharton RA,Wirkner CS,Woolley JB,Yoder MJ,Zorn AM,Mabee P
PLoS Biol 2015