Table 4.
List of comprehensive metabolomic databases
| Link of the databases | Teams or specificity | Numbers of metabolites | Data included |
|---|---|---|---|
| BIGG (
http://bigg.ucsd.edu) |
A metabolic reconstruction of human metabolism |
1,496 ORFs*1, 2,004 proteins, 2,766 metabolites, and 3,331 metabolic and transport reactions |
Literature-based genome-scale metabolic reconstruction |
| BinBase (
http://bigg.ucsd.edu/) |
A GC-TOF*2 metabolomic database |
Unknown |
Metabolomic database |
| HMDB (
http://www.hmdb.ca) |
Human Metabolome Database; |
More than 6,500; |
Chemical data; Clinical data; Molecular Biology/Biochemistry data |
| |
Small molecule metabolites |
Link to ~ 1,500 protein and DNA sequences |
|
| SetupX (
http://bigg.ucsd.edu/;
http://fiehnlab.ucdavis.edu:8080/m1/readme.jsp) |
A web-based metabolomics LIMS*3 |
unknown |
Display of GC-MS*4 metabolomic data |
| SMPDB (
http://www.smpdb.ca/) |
The small molecule pathway database |
More than 350 small molecule pathways |
Human metabolic pathways, metabolic disease pathways, metabolite signaling pathways and drug-action pathways |
| SYSTOMONAS ( http://fiehnlab.ucdavis.edu:8080/m1/login.jsp) | Systems biology of pseudomonas--systems biology studies of Pseudomonas species. | Extensive | Transcriptomics, proteomic, metabolomic and metabolic reconstructions |
Abbreviations: *1ORFs: open reading frames; *GC-TOF: gas chromatography/time-of-flight; *3 LIMS: laboratory information management system; *4 GC/MS: Gas chromatograph/ mass spectrometry.