Table 6.
Well-established, recommended platforms | Promising platforms | |||||||
---|---|---|---|---|---|---|---|---|
Tripal | InterMine | Germinate | GenomeHubs/Ensembl | SGN | T3 | Reactome | ||
Feature category | Feature type | Chado & PostgreSQL | PostgreSQL | MySQL | MySQL | Chado & PostgreSQL | MySQL | GraphDb (neo4J) |
Query | Simple full site keyword search | 2 | 2 | 2 | 2 | 2 | 2 | 2 |
Question-based searches (set up by administrator) | 2 | 2 | 2 | x | x | 2 | x | |
Simple advanced searches (multiple fixed filter criteria) | 2 | 2 | 2 | x | 2 | 2 | 2 | |
Query-builder advanced search | x | 2 | 2 | x | 2 | 2 | 2 | |
List support | 1 | 2 | 2 | x | 2 | 2 | x | |
Genomic region search/overlap queries | 1 | 2 | 1 | 2 | 1 | 1 | x | |
Browsing | Basic browsing | 2 | 2 | 2 | 2 | 2 | 2 | 2 |
Data information pages (e.g. gene pages) | 2 | 2 | 2 | 2 | 2 | 2 | 2 | |
Data type-specific summaries | 1 | 2 | 2 | 2 | 2 | 2 | 2 | |
Community | Forum | 1 | x | 1 | x | 2 | 1 | x |
Conference pages | 2 | 1 | 1 | x | x | x | x | |
Community news | 2 | 2 | 2 | x | 2 | 2 | x | |
Community curation | 2 | x | x | x | 2 | x | x | |
Community information pages | 2 | 1 | 2 | x | 2 | x | x | |
Data sharing | Web services | 2 | 2 | 2 | 2 | 2 | 2 | 2 |
Query across sites | 2 | 2 | 1 | x | 2 | 1 | 2 | |
Reference sister sites | 2 | 2 | 2 | 2 | 2 | 2 | 2 | |
Other | Genome browser integration | 1 | 2 | 1 | 2 | 2 | 1 | x |
BLAST integration | 1 | 1 | 1 | 2 | 2 | 1 | x | |
Access control (login system) | 2 | 2 | 2 | 2 | 2 | 2 | x | |
Data analysis tools | 1 | 1 | 2 | 2 | 2 | 2 | 2 |