Table 5.
Data types and their support by each GGB platform. The following table rates support for each data type using the following scale: (x) No Support, (i) Schema Support Only, (ii) Extension Module Support and (iii) Core Interface Support. Core interface support implies the core application supports this data by providing loaders and front–end visualization. Extension module support implies this functionality has been added by some groups using the application and is now available in a sharable format (extension module or detailed tutorial). Schema Support Only implies the database schema can store this type of data but as of yet, no loaders or front–end visualizations are available
| Well-established, recommended platforms | Promising platforms | |||||||
|---|---|---|---|---|---|---|---|---|
| Tripal | InterMine | Germinate | GenomeHubs/Ensembl | SGN | T3 | Reactome | ||
| Data category | Data type | Chado & PostgreSQL | PostgreSQL | MySQL | MySQL | Chado & PostgreSQL | MySQL | GraphDb (neo4J) |
| Genomic | Assembly | 3 | 3 | x | 3 | 3 | 2 | x |
| Gene annotation | 3 | 3 | x | 3 | 2 | 2 | x | |
| Gene–gene interactions | 1 | 3 | x | x | 2 | x | x | |
| Protein domains | 1 | 3 | x | 3 | 2 | x | x | |
| HTS Gene expression data | 2 | 2 | x | 3 | 3 | x | x | |
| Array-based gene expression data | 1 | 2 | x | x | x | x | x | |
| RNA-seq | 2 | 2 | x | 3 | 2 | x | x | |
| Diversity | Genomic variation (copy #, translocations, SNPs) | 1 | 2 | x | 3 | 3 | 3 | x |
| Genotypic data (alleles, polymorphisms) | 2 | 3 | 3 | 3 | 3 | 3 | x | |
| Phenotypic data | 2 | 2 | 3 | 3 | 3 | 3 | x | |
| QTL | 3 | 2 | x | x | 3 | 2 | x | |
| Mutants (fast neutron, transposon, Ethyl methanesulfonate (EMS)) | x | x | x | x | 3 | x | x | |
| Phylogeny | 3 | 2 | x | 3 | 2 | x | x | |
| Comparative analyses | 1 | 1 | x | 3 | 3 | x | x | |
| Germplasm management & breeding | Germplasm Stocks | 3 | 3 | x | x | 3 | x | x |
| Germplasm (Varieties, Landraces etc.) | 3 | 2 | 3 | x | 3 | 3 | x | |
| Germplasm pedigrees | 2 | 2 | 3 | x | 3 | 3 | x | |
| Genetic maps | 2 | 2 | 3 | x | 3 | 3 | x | |
| Field trial Data | 1 | 1 | 3 | x | 3 | 3 | x | |
| Other | Pathways | x | 3 | x | 2 | 2 | 2 | 3 |
| Images | 2 | 2 | 3 | x | 3 | x | x | |
| Ontology | 3 | 3 | x | 2 | 3 | 3 | x | |
| Ontology-based annotations | 3 | 3 | x | 3 | 3 | 3 | x | |