Together with the plugin-based structure of V anted, it is easy to extend the functionality even at run time, such as additional database access, e.g. MetaCrop (Grafahrend-Belau et al., 2008) and DBE (Borisjuk et al., 2005), simulation capabilities, e.g. flux balance analysis (Kauffman et al., 2003), mapping functions and visualization algorithms.
We extended this initial set of reactions by including further KEGG reactions [ 91] associated with EC numbers that are annotated as present in heart tissue by additional databases such as the Braunschweig Enzyme database (BRENDA) [ 92] and UniProtKB [ 93].
BIND records often contained references to additional databases, such as ChEBI for small molecules.
We chose to develop a new genome browser instead of adopting one of the existing browsers in part because the adoption required conversion of the data archived in CFGP into new formats, and the existing browsers do not support the integration of additional databases, such as the InterPro and customized homologous gene databases available through SNUGB.
For linking bio-entities to biological databases, i.e. entity normalization, Entrez Gene and UniProt were set up as default; however, additional databases can be added as well through the web interface.
Combining MirSNP with additional databases containing expression information, such as miRGator [ 41], would improve the functionality of the database.
Additional databases such as GO, COG (7, 8), IntAct (9), NCBI Mesh terms and MIT BioBricks are integrated as well as the connection to Cytoscape (26).
Additional databases such as the Discharge Abstract Database (DAD) for patients' hospitalizations, the Medical Services Billing Claims Data (MSB) for the physician visits, the Personal Health Registration System PHRSS) for patient demographics and location of residence, and Vital Statistics Registry for death information were utilized in this study.
What is currently annotated explains a minute fraction of the complexity found in these regions, both in terms of the base pair coverage and fraction of reads, even if we include additional databases, such as RefSeq, Ensemble and all spliced ESTs.
Although the searches identified over 10 000 initial records, they could have been made more sensitive through greater use of techniques such as truncation, synonyms and by searching additional databases.
As molecular sequence databases became increasingly prevalent and used by researchers, additional databases were included in the curation workflow over the years.
