Innovating the wheat community through the RDA services and outputs

AGRIS Linked Open Data

AGRIS Linked Open Data: This dataset include more than 8 millions bibliographic references for agricultural research. The SPARQL end point is http://202.45.139.84:10035/catalogs/fao/repositories/agris#query

CIARD RING

CIARD RING (ring.ciard.info): registry of open datasets for agricultural and food sector. The registry can be also accessed using machine interface

Food safety alerts and recalls

Food safety alerts and recalls: More than 40.000 food safety notifications available through https://webgate.ec.europa.eu/rasff-window/portal/?event=SearchForm&cleanSearch=1#

Open Educational Resources

Open Educational Resources: This end point includes more than 20.000 open educational resources related to agriculture and food topics http://api.akstem.com/search-api/.

AGROVOC

AGROVOC: a semantic multilingual vocabulary for agricultural topics (http://aims.fao.org/vest-registry/vocabularies/agrovoc-multilingual-agricultural-thesaurus). It can be used to annotate resources and to connect them with other linked open data sources e.g. DBpedia. AGROVOC can be downloaded in RDF format from: https://aims-fao.atlassian.net/wiki/display/AGV/Releases

Foodborne outbreaks

Foodborne outbreaks data from Centers for Disease Control and Prevention (https://data.cdc.gov/)

Eurostat Datasets

Several agricultural and economical indicators from eurostat. These are available in tsv format from the following url: http://ec.europa.eu/eurostat/web/regions/data/database

AGROVOC

AGROVOC (a portmanteau of agriculture and vocabulary) is a multilingual controlled vocabulary covering all areas of interest to the Food and Agriculture Organization of the United Nations (FAO), including food, nutrition, agriculture, fisheries, forestry and the environment. The vocabulary consists of over 32,000 concepts with up to 40,000 terms in 23 languages: Arabic, Chinese, Czech, English, French, German, Hindi, Hungarian, Italian, Japanese, Korean, Lao, Malay, Persian, Polish, Portuguese, Russian, Slovak, Spanish, Telugu, Thai, Turkish and Ukrainian. It is a collaborative effort, edited by a community of experts and coordinated by FAO. You can download the AGROVOC vocabulary here

Eurostat Wheat Datasets

The domain EUROFARM (ef)Â contains information (statistical tables) on structure of agricultural holdings collected through agricultural structure surveys. The data of the domain have been organised into two collections:

Results of the farm structure surveys contains data from 1990 onwards based on the 1988 legislation and

Results of the farm structure surveys based on the legislation from 2008. This collection contains the data from the 2010 Census onwards as well as the data for the surveys 2007 and 2005.

following url: https://knoema.com/ef_alwheat/common-wheat-number-of-farms-and-areas-by-agricultural-size-of-farm-uaa-and-size-of-common-wheat-are

GNPIS

The International Wheat Genome Sequencing Consortium provides genome maps regarding wheat. repository containe The data and their description are accessible here: https://wheat-urgi.versailles.inra.fr/Seq-Repository The data are also accessible through web services (https://urgi.versailles.inra.fr/Tools/Web-services) and the breeding API (please see the enclosed presentation of the breeding API). Click here to download a presentation which presents the GNPIS information system and particularly phenotyping data in GNPIS.

Cerealdb

Wheat genome sequences made available as part of a collaboration with the John Innes Centre and the Universities of Bristol and Liverpool. They can be downloaded here : http://www.cerealsdb.uk.net/cerealgenomics/CerealsDB/copyright.php An API is available for access to SNPs and contigs here : http://www.cerealsdb.uk.net/cerealgenomics/CerealsDB/web_API.php

Ensembl Triticum aestivum data

This dataset contains genome assemblies, gene annotations, comparative genomics, and variations of Triticum aestivum (bread wheat). It can be accessed and dowloaded here: http://plants.ensembl.org/Triticum_aestivum/Info/Index

T3 Wheat

This dataset contains genotype and phenotype data, SNP Alleles and sequences, marker annotation data, android field.

The Triticeae Toolbox (T3) is the web portal for data generated by the Triticeae Coordinated Agricultural Project (T-CAP), funded by the National Institute for Food and Agriculture (NIFA) of the United States Department of Agriculture (USDA). The database, developed initially as The Hordeum Toolbox (THT) to hold barley data generated by the Barley CAP project (2006-2010) is being maintained as T3 Barley while a sister database T3 Wheat will hold data generated for Triticum spp. Both are being enhanced in database performance, community curation and user tools. T3 contains germplasm line information, pedigree, genotype and phenotypic data from breeding programs participating in the CAP and core germplasm collections maintained by the USDA National Small Grains Collection.

It can be downloaded from here: https://triticeaetoolbox.org/wheat/

PlantsDB Databases

The PGSB plant genomics group focuses on the analysis of plant genomes, using bioinformatic techniques. To store and manage the data, we developed a database, PlantsDB, that aims to provide a data and information resource for individual plant species. In addition PlantsDB provides a platform for integrative and comparative plant genome research. The databases are organizes per species and can be accessed/downloaded here: http://pgsb.helmholtz-muenchen.de/plant/plantsdb.jsp

Gramene / Ensembl

Data (and file formats) available for the plant reference genomes in Gramene and Ensembl Plants include:

DNA, cDNA and Protein (FASTA)

Genomic DNA sequence (EMBL and GenBank flatfile dumps)

Ensembl core databases and specific features (MySQL and simple text format)

Species-centered data including comparative genomics annotations (TSV)

Gene annotations (GTF and GFF3)

Variation data (GVF and VCF)

It can be accessed and downloaded here: http://plants.ensembl.org/info/website/ftp/index.html