RESUMEN
We present the design and implementation of a semantics-enabled service discovery framework in the data Grids for process and product development using numerical simulation and knowledge discovery (SIMDAT) Pharma Grid, an industry-oriented Grid environment for integrating thousands of Grid-enabled biological data services and analysis services. The framework consists of three major components: the Web ontology language (OWL)-description logic (DL)-based biological domain ontology, OWL Web service ontology (OWL-S)-based service annotation, and semantic matchmaker based on the ontology reasoning. Built upon the framework, workflow technologies are extensively exploited in the SIMDAT to assist biologists in (semi)automatically performing in silico experiments. We present a typical usage scenario through the case study of a biological workflow: IXodus.
Asunto(s)
Conducta Cooperativa , Sistemas de Administración de Bases de Datos , Sistemas de Liberación de Medicamentos/métodos , Diseño de Fármacos , Internet , Procesamiento de Lenguaje Natural , Mapeo de Interacción de Proteínas/métodos , Semántica , Difusión de la Información/métodosRESUMEN
Organization of proteins into complexes is crucial for many cellular functions. However, most proteomic approaches primarily detect protein interactions for soluble proteins but are less suitable for membrane-associated complexes. Here we describe a mating-based split ubiquitin system (mbSUS) for systematic identification of interactions between membrane proteins as well as between membrane and soluble proteins. mbSUS allows in vivo cloning of PCR products into a vector set, detection of interactions via mating, regulated expression of baits, and improved selection of interacting proteins. Cloning is simplified by introduction of lambda attachment sites for GATEWAY. Homo- and heteromeric interactions between Arabidopsis K(+) channels KAT1, AKT1, and AKT2 were identified. Tests with deletion mutants demonstrate that the C terminus of KAT1 and AKT1 is necessary for physical assembly of complexes. Screening of a sorted collection of 84 plant proteins with K(+) channels as bait revealed differences in oligomerization between KAT1, AKT1, and AtKC1, and allowed detection of putative interacting partners of KAT1 and AtKC1. These results show that mbSUS is suited for systematic analysis of membrane protein interactions.