Table 2 Overview of the use-cases in the SigPath Benchmark
Project stage | Step | Utility for the SigPath project |
|---|---|---|
development | boot | Loads a sample set of information that can be used to run JUnit tests and for interactive testing of the web application |
development | test | Performs JUnit tests to verify that key aspects of the system are working correctly |
pre-release | SM import | Import small molecule information (names, aliases SMILES from NCI Open) |
pre-release | Full Text Indexer 1 | Builds an inverted full text index for small molecules imported in previous step |
pre-release | mam.xml | Imports TREMBL mam.dat proteins |
pre-release | rod.xml | Imports TREMBL hum.dat proteins |
pre-release | hum.xml | Imports TREMBL inv.dat proteins |
pre-release | inv.xml | Imports TREMBL inv.dat proteins |
pre-release | vrt.xml | Imports TREMBL vrt.dat proteins |
pre-release | sprot41_1.xml | import SwissProt 41.dat, part I |
pre-release | sprot41_2.xml | import SwissProt 41.dat, part II |
pre-release | Full Text Indexer 2 | Builds an inverted full text index for the proteins imported from TrEMBL and SwissProt |
pre-release | XML Import | Imports data from another SigPath database (data is encoded in the SigPath XML exchange format) |
traversal simulation | TestGetPathways | Navigates through the Pathway instances. Used to simulate user navigation on the web site. |
traversal simulation | TestBenchmark | Another benchmark-specific performance test. |