Table 3

EC number content of Swiss-Prot, TrEMBL, PIR, CMR, and BioCyc. Total EC numbers is the number of distinct EC numbers in each DB. Incremental Novel ECnumbers is the number of EC numbers present in a given DB that were not present in all preceding DBs in the table. For example, 158 EC numbers are present in PIR that are not present in either Swiss-Prot or TrEMBL. We do not show all pairwise combinations of shared EC numbers between DBs because it is not particularly meaningful. Time is the execution time of the SQL query listed below to compute the distinct EC numbers in each DB on a dual-CPU 1 GHz Pentium Oracle server with 2 GB memory running Linux. Note that because a PIR warehouse loader does not exist at this time, PIR statistics were obtained through queries to an XML version of PIR outside the warehouse. Note also that it is somewhat surprising that PIR contains EC numbers not found in Swiss-Prot, because version 42.6 is a UniProt version of Swiss-Prot that incorporates data from PIR. It appears that not all data from PIR entries has been incorporated into UniProt.

Database

Version

Total EC numbers

Incremental Novel EC numbers

Time


Swiss-Prot

42.6

1899

1899

7.6 s

TrEMBL

25.4

1678

316

53 s

PIR

PIR-PSD 78.03

1695

108

na

CMR

April, 2003

1230

26

159 s

BioCyc

7.6

1357

44

2.6 s


Lee et al. BMC Bioinformatics 2006 7:170   doi:10.1186/1471-2105-7-170

Open Data