Table 1 Comparison of different databases, which could be used to annotate and analyze large-scale biological data. Simplified joins refers to the availability of a central key and the ability to join tables through simple queries. Remote access column refers only to a machine access to a database server.
From: GeneKeyDB: A lightweight, gene-centric, relational database to support data mining environments
Database | SQL | Web interface | Simplified joins | 1Remote access | Automatic updates provided | Type | Structure available as | Modular design | Download |
|---|---|---|---|---|---|---|---|---|---|
GeneKeyDB | Yes | 2Indirect | Yes | No | Yes | Oracle | Oracle, mysql, postgresql | Yes | Yes |
LocusLink (Entrez Gene) | No | Yes | Na | Na | No | Flat file(s) | Flat file only | Na | Yes |
RefSeq | No | Yes | Na | Na | No | Flat file | Flat file only | Na | Yes |
Ensembl (core databases) | Yes | Yes | No | Yes | No | Mysql | Mysql | No | Yes |
EnsMART | Yes | Yes | Yes | Yes | No | Mysql | Mysql | No | Yes |
Dragon | Yes | Yes | No | No | No | Mysql | Flat file only | No | Data files only |
HomoloGene | No | Yes | Na | Na | No | Flat files, XML | XML | No | Yes |