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Table 2 Overview of the use-cases in the SigPath Benchmark

From: Critical evaluation of the JDO API for the persistence and portability requirements of complex biological databases

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.