DASMI: exchanging, annotating and assessing molecular interaction data

Abstract

Motivation: Ever increasing amounts of biological interaction data are being accumulated worldwide, but they are currently not readily accessible to the biologist at a single site. New techniques are required for retrieving, sharing and presenting data spread over the Internet.

Results: We introduce the DASMI system for the dynamic exchange, annotation and assessment of molecular interaction data. DASMI is based on the widely used Distributed Annotation System (DAS) and consists of a data exchange specification, web servers for providing the interaction data and clients for data integration and visualization. The decentralized architecture of DASMI affords the online retrieval of the most recent data from distributed sources and databases. DASMI can also be extended easily by adding new data sources and clients. We describe all DASMI components and demonstrate their use for protein and domain interactions.

Availability: The DASMI tools are available at http://www.dasmi.de/ and http://ipfam.sanger.ac.uk/graph. The DAS registry and the DAS 1.53E specification is found at http://www.dasregistry.org/.

Fig. 1.

Levels of molecular interactions. Physical and non-physical interaction types can be distinguished: (a) Non-physical interactions are based on functional associations. (b) Physical interactions imply a direct physical contact between the interacting molecules like proteins, domains or small ligands. (c) Raising the level of detail to 3D structural data, the interacting atoms or residues of binding sites can be identified.

Fig. 2.

Schematic DASMI system architecture. The DASMI architecture is similar to the original DAS architecture (Dowell et al., 2001). Interaction servers provide interactions (Interaction Server 1) and, optionally, additional information like experimental conditions (Interaction Server 2). Confidence servers provide confidence scores for interactions (Confidence Server 1). DASMI clients query interaction servers and combine their results. The DAS registry maintains a list of available DAS servers.

Fig. 3.

Exemplary interaction request and DASINT response. The communication between DASMI server and client is performed using formatted URL requests and XML responses. (a) Interactions are requested using the interaction command. In the example shown here, all protein interactions involving the proteins P09497 and O60828 and annotated with a BPscore would be retrieved. (b) The server response is a DASINT XML format. (c) Overview of the DASINT XML Schema Definition. Mandatory elements are marked using solid frames, optional elements have dashed frames.

Fig. 4.

DASMI clients DASMIweb and iPfam. (a) DASMIweb is an online tool for dynamically unifying protein and domain interaction data and additional annotations. The results are presented in tabular form: each column represents a DASMI server, each row contains an interaction partner, and squares at the intersections of rows and columns indicate interactions. In this figure, the interaction squares are colored according to the functional similarity between the interacting proteins, from dark blue for high to white for low similarity. (b) The iPfam client tool combines domain–domain interactions from several sources with interactions reported in the iPfam database. The results are presented in graphical form; protein domains are depicted as ovals and interactions as edges that connect ovals. Different edge colors distinguish individual data sources.