Before revision:  We have developed ppiTrim, a script that can process iRefIndex to produce a consolidated dataset of physical interactions for, in principle, every URLanism. For the current publication we processed only the three largest datasets: yeast, human and fruitfly. ppiTrim maps interactants to NCBI Gene IDs, deflates possibly spoke-expanded complexes and reconciles annotation labels between different source databases.
After revision:  We have developed ppiTrim, a script that can process iRefIndex to produce a consolidated dataset of physical interactions . Our script proceeds in three stages: mapping all interactants to gene identifiers and removing all undesired raw interactions, deflating potentially expanded complexes, and reconciling for each interaction the annotation labels among different source databases. As an illustration, we have processed the three URLanismal datasets: yeast, human and fruitfly. ppiTrim maps interactants to NCBI Gene IDs, deflates possibly spoke-expanded complexes and reconciles annotation labels between different source databases.