Table 2.
Server implementations
| Database name | URLs | Organization, Reference |
|---|---|---|
| Breeding Management System (BMS) | https://www.integratedbreeding.net | CGIAR https://cgiar.org |
| Description: comprehensive breeding management system with trial design, data collection, and analyses. | ||
|
|
|
| Description: comprehensive breeding management system, including trial design management, phenotyping sample and data collection; with a focus on genomic breeding technologies such as Genomic Selection | ||
| B4R | https://b4r.irri.org | International Rice Research Institute (IRRI), http://irri.org |
| Description: comprehensive breeding management system tailored for rice and other grains | ||
| Germinate | https://ics.hutton.ac.uk/get-germinate | The James Hutton Institute, http://hutton.ac.uk |
| Description: breeding database and analysis tools | ||
| GOBii | http://gobiiproject.org |
|
| Description: large scale and efficient genotyping storage system including data analysis workflows | ||
| T3 | https://triticeaetoolbox.org | USDA, https://usda.gov |
| Description: comprehensive breeding management system designed for wheat | ||
| Musa Germplasm Information System (MGIS) | https://www.crop-diversity.org/mgis | Bioversity International, https://bioversityinternational.org, (Ruas et al., 2017) |
| Description: information system on banana germplasm | ||
| Gigwa | http://gigwa.southgreen.fr | CIRAD, IRD (South Green) |
| Description: Gigwa (Sempéré et al., 2016) is a web-application that aims at storing and exposing genotypic datasets and provides a web interface for filtering them in real time. It is able to interoperate with genome browsers and export results into several formats. | ||
| EU-SOL Database | https://www.eu-sol.wur.nl | Wageningen University & Research, https://wur.nl |
| Description: this site contains information about a collection composed of ∼7000 domesticated (S. lycopersicum) lines, along with representative wild species, collected with the scope of the european project EU-SOL. This germplasm was generously provided by different international genebanks and by donations from private collections. This Integrated Project is supported by the European Commission through the 6th framework program. Contract number: FOOD-CT-2006-016214 | ||
| GnpIS | https://urgi.versailles.inra.fr/gnpis | INRA, https://www.inra.fr |
| Description: French national archive for plant phenotyping data. It provides any type of PGR and Phenotyping data. Used for instance by Perpheclim for climate change adaptation studies and as a data repository in the Elixir federation which is under construction. It contains almost a thousand Phenotyping trials over thousands of woody and annual plant varieties. | ||
| KDDart | https://kddart.diversityarrays.com/brapi/v1/ | DArT, http://www.kddart.org |
| Description: genotype and phenotype database, linked to genotyping service | ||
| Crop Ontology | http://www.cropontology.org/ | Bioversity, https://bioversityinternational.org |
| Description: database of available trait ontologies for diverse crops in the CGIAR system | ||
| PIPPA | https://pippa.psb.ugent.be | VIB https://www.psb.ugent.be/ |
| Description: PSB Interface for Plant Phenotype Analysis | ||
| PHIS | http://www.phis.inra.fr | INRA, https://www.inra.fr |
| Description: ontology-driven Information System designed for Plant Phenomics. PHIS is designed to store, organize and manage highly heterogeneous and multi-spatial and temporal data from multiple sources (field, greenhouse). | ||
| GBIS/I | https://fair-ipk.ipk-gatersleben.de/public/breedingapi.html | IPK-Gatersleben, https://www.ipk-gatersleben.de |
| Description: among other, FAIR-IPK offers access to IPK genbank information system GBIS. This comprise passport data (information on the identity, history, geographical origin and botanical classification of the material) of the 150, 780 accessions in Gatersleben (as of 30 June 2016), including the Satellite Collections North in Gross Lüsewitz (potatoes) and Malchow/Poel (oil and fodder crops). | ||
| TERRA REF | https://terraref.ncsa.illinois.edu/bety | https://terraref.org |
| Description: an open access reference database for high throughput phenomics. Crops include sorghum and wheat. | ||